diff --git a/revdep/README.md b/revdep/README.md new file mode 100644 index 0000000..616a278 --- /dev/null +++ b/revdep/README.md @@ -0,0 +1,30 @@ +# Platform + +|field |value | +|:--------|:-----------------------------------| +|version |R version 4.3.2 (2023-10-31) | +|os |macOS Sonoma 14.3.1 | +|system |x86_64, darwin20 | +|ui |RStudio | +|language |(EN) | +|collate |en_US.UTF-8 | +|ctype |en_US.UTF-8 | +|tz |America/New_York | +|date |2024-03-11 | +|rstudio |2023.12.1+402 Ocean Storm (desktop) | +|pandoc |2.8.0.1 @ /usr/local/bin/pandoc | + +# Dependencies + +|package |old |new |Δ | +|:-------|:-----|:----------|:--| +|LDlinkR |1.3.0 |1.3.0.9002 |* | + +# Revdeps + +## Failed to check (1) + +|package |version |error |warning |note | +|:-------|:-------|:-----|:-------|:----| +|GRaNIE |? | | | | + diff --git a/revdep/checks.noindex/libraries.csv b/revdep/checks.noindex/libraries.csv new file mode 100644 index 0000000..26a1f1c --- /dev/null +++ b/revdep/checks.noindex/libraries.csv @@ -0,0 +1,2 @@ +package,old,new,delta +LDlinkR,1.3.0,1.3.0.9002,* diff --git a/revdep/checks.noindex/locuszoomr/locuszoomr_0.2.1.tar.gz b/revdep/checks.noindex/locuszoomr/locuszoomr_0.2.1.tar.gz new file mode 100644 index 0000000..ae474f6 Binary files /dev/null and b/revdep/checks.noindex/locuszoomr/locuszoomr_0.2.1.tar.gz differ diff --git a/revdep/checks.noindex/locuszoomr/new/libraries.txt b/revdep/checks.noindex/locuszoomr/new/libraries.txt new file mode 100644 index 0000000..17bb84a --- /dev/null +++ b/revdep/checks.noindex/locuszoomr/new/libraries.txt @@ -0,0 +1,135 @@ +Library: /Users/myersta/Library/CloudStorage/OneDrive-NationalInstitutesofHealth/Rprojects_OneDrive/ldlinkr/revdep/library.noindex/LDlinkR/new +LDlinkR (1.3.0.9002) + +Library: /Users/myersta/Library/CloudStorage/OneDrive-NationalInstitutesofHealth/Rprojects_OneDrive/ldlinkr/revdep/library.noindex/locuszoomr +abind (1.4-5) +AnnotationDbi (1.64.1) +AnnotationFilter (1.26.0) +AnnotationHub (3.10.0) +askpass (1.2.0) +base64enc (0.1-3) +Biobase (2.62.0) +BiocFileCache (2.10.1) +BiocGenerics (0.48.1) +BiocIO (1.12.0) +BiocParallel (1.36.0) +BiocVersion (3.18.1) +biomaRt (2.58.2) +Biostrings (2.70.2) +bit (4.0.5) +bit64 (4.0.5) +blob (1.2.4) +bslib (0.6.1) +cli (3.6.2) +codetools (0.2-19) +colorspace (2.1-0) +commonmark (1.9.1) +crayon (1.5.2) +crosstalk (1.2.1) +data.table (1.15.2) +DBI (1.2.2) +dbplyr (2.4.0) +DelayedArray (0.28.0) +digest (0.6.34) +EnsDb.Hsapiens.v75 (2.99.0) +ensembldb (2.26.0) +evaluate (0.23) +fansi (1.0.6) +farver (2.1.1) +fastmap (1.1.1) +filelock (1.0.3) +fontawesome (0.5.2) +formatR (1.14) +fs (1.6.3) +generics (0.1.3) +GenomeInfoDb (1.38.7) +GenomeInfoDbData (1.2.11) +GenomicAlignments (1.38.2) +GenomicFeatures (1.54.3) +GenomicRanges (1.54.1) +gggrid (0.2-0) +ggplot2 (3.5.0) +ggrepel (0.9.5) +glue (1.7.0) +gtable (0.3.4) +highr (0.10) +hms (1.1.3) +htmltools (0.5.7) +htmlwidgets (1.6.4) +httpuv (1.6.14) +httr (1.4.7) +interactiveDisplayBase (1.40.0) +IRanges (2.36.0) +isoband (0.2.7) +jquerylib (0.1.4) +jsonlite (1.8.8) +KEGGREST (1.42.0) +knitr (1.45) +labeling (0.4.3) +lambda.r (1.2.4) +later (1.3.2) +lattice (0.22-5) +lazyeval (0.2.2) +lifecycle (1.0.4) +magrittr (2.0.3) +MASS (7.3-60.0.1) +Matrix (1.6-5) +MatrixGenerics (1.14.0) +matrixStats (1.2.0) +memoise (2.0.1) +mgcv (1.9-1) +mime (0.12) +munsell (0.5.0) +nlme (3.1-164) +openssl (2.1.1) +pillar (1.9.0) +pkgconfig (2.0.3) +plogr (0.2.0) +plotly (4.10.4) +png (0.1-8) +prettyunits (1.2.0) +progress (1.2.3) +promises (1.2.1) +ProtGenerics (1.34.0) +purrr (1.0.2) +R6 (2.5.1) +rappdirs (0.3.3) +RColorBrewer (1.1-3) +Rcpp (1.0.12) +RCurl (1.98-1.14) +restfulr (0.0.15) +Rhtslib (2.4.1) +rjson (0.2.21) +rlang (1.1.3) +rmarkdown (2.26) +Rsamtools (2.18.0) +RSQLite (2.3.5) +rtracklayer (1.62.0) +S4Arrays (1.2.1) +S4Vectors (0.40.2) +sass (0.4.8) +scales (1.3.0) +shiny (1.8.0) +snow (0.4-4) +sourcetools (0.1.7-1) +SparseArray (1.2.4) +stringi (1.8.3) +stringr (1.5.1) +SummarizedExperiment (1.32.0) +sys (3.4.2) +tibble (3.2.1) +tidyr (1.3.1) +tidyselect (1.2.0) +tinytex (0.49) +utf8 (1.2.4) +vctrs (0.6.5) +viridisLite (0.4.2) +withr (3.0.0) +xfun (0.42) +XML (3.99-0.16.1) +xml2 (1.3.6) +xtable (1.8-4) +XVector (0.42.0) +yaml (2.3.8) +zlibbioc (1.48.0) +zoo (1.8-12) diff --git a/revdep/checks.noindex/locuszoomr/new/locuszoomr.Rcheck/00check.log b/revdep/checks.noindex/locuszoomr/new/locuszoomr.Rcheck/00check.log new file mode 100644 index 0000000..0b1b012 --- /dev/null +++ b/revdep/checks.noindex/locuszoomr/new/locuszoomr.Rcheck/00check.log @@ -0,0 +1,20 @@ +* using log directory ‘/Users/myersta/Library/CloudStorage/OneDrive-NationalInstitutesofHealth/Rprojects_OneDrive/ldlinkr/revdep/checks.noindex/locuszoomr/new/locuszoomr.Rcheck’ +* using R version 4.3.2 (2023-10-31) +* using platform: x86_64-apple-darwin20 (64-bit) +* R was compiled by + Apple clang version 14.0.0 (clang-1400.0.29.202) + GNU Fortran (GCC) 12.2.0 +* running under: macOS Sonoma 14.3.1 +* using session charset: UTF-8 +* using options ‘--no-manual --no-build-vignettes’ +* checking for file ‘locuszoomr/DESCRIPTION’ ... OK +* this is package ‘locuszoomr’ version ‘0.2.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘cowplot’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR diff --git a/revdep/checks.noindex/locuszoomr/old/libraries.txt b/revdep/checks.noindex/locuszoomr/old/libraries.txt new file mode 100644 index 0000000..81d10f8 --- /dev/null +++ b/revdep/checks.noindex/locuszoomr/old/libraries.txt @@ -0,0 +1,135 @@ +Library: /Users/myersta/Library/CloudStorage/OneDrive-NationalInstitutesofHealth/Rprojects_OneDrive/ldlinkr/revdep/library.noindex/LDlinkR/old +LDlinkR (1.3.0) + +Library: /Users/myersta/Library/CloudStorage/OneDrive-NationalInstitutesofHealth/Rprojects_OneDrive/ldlinkr/revdep/library.noindex/locuszoomr +abind (1.4-5) +AnnotationDbi (1.64.1) +AnnotationFilter (1.26.0) +AnnotationHub (3.10.0) +askpass (1.2.0) +base64enc (0.1-3) +Biobase (2.62.0) +BiocFileCache (2.10.1) +BiocGenerics (0.48.1) +BiocIO (1.12.0) +BiocParallel (1.36.0) +BiocVersion (3.18.1) +biomaRt (2.58.2) +Biostrings (2.70.2) +bit (4.0.5) +bit64 (4.0.5) +blob (1.2.4) +bslib (0.6.1) +cli (3.6.2) +codetools (0.2-19) +colorspace (2.1-0) +commonmark (1.9.1) +crayon (1.5.2) +crosstalk (1.2.1) +data.table (1.15.2) +DBI (1.2.2) +dbplyr (2.4.0) +DelayedArray (0.28.0) +digest (0.6.34) +EnsDb.Hsapiens.v75 (2.99.0) +ensembldb (2.26.0) +evaluate (0.23) +fansi (1.0.6) +farver (2.1.1) +fastmap (1.1.1) +filelock (1.0.3) +fontawesome (0.5.2) +formatR (1.14) +fs (1.6.3) +generics (0.1.3) +GenomeInfoDb (1.38.7) +GenomeInfoDbData (1.2.11) +GenomicAlignments (1.38.2) +GenomicFeatures (1.54.3) +GenomicRanges (1.54.1) +gggrid (0.2-0) +ggplot2 (3.5.0) +ggrepel (0.9.5) +glue (1.7.0) +gtable (0.3.4) +highr (0.10) +hms (1.1.3) +htmltools (0.5.7) +htmlwidgets (1.6.4) +httpuv (1.6.14) +httr (1.4.7) +interactiveDisplayBase (1.40.0) +IRanges (2.36.0) +isoband (0.2.7) +jquerylib (0.1.4) +jsonlite (1.8.8) +KEGGREST (1.42.0) +knitr (1.45) +labeling (0.4.3) +lambda.r (1.2.4) +later (1.3.2) +lattice (0.22-5) +lazyeval (0.2.2) +lifecycle (1.0.4) +magrittr (2.0.3) +MASS (7.3-60.0.1) +Matrix (1.6-5) +MatrixGenerics (1.14.0) +matrixStats (1.2.0) +memoise (2.0.1) +mgcv (1.9-1) +mime (0.12) +munsell (0.5.0) +nlme (3.1-164) +openssl (2.1.1) +pillar (1.9.0) +pkgconfig (2.0.3) +plogr (0.2.0) +plotly (4.10.4) +png (0.1-8) +prettyunits (1.2.0) +progress (1.2.3) +promises (1.2.1) +ProtGenerics (1.34.0) +purrr (1.0.2) +R6 (2.5.1) +rappdirs (0.3.3) +RColorBrewer (1.1-3) +Rcpp (1.0.12) +RCurl (1.98-1.14) +restfulr (0.0.15) +Rhtslib (2.4.1) +rjson (0.2.21) +rlang (1.1.3) +rmarkdown (2.26) +Rsamtools (2.18.0) +RSQLite (2.3.5) +rtracklayer (1.62.0) +S4Arrays (1.2.1) +S4Vectors (0.40.2) +sass (0.4.8) +scales (1.3.0) +shiny (1.8.0) +snow (0.4-4) +sourcetools (0.1.7-1) +SparseArray (1.2.4) +stringi (1.8.3) +stringr (1.5.1) +SummarizedExperiment (1.32.0) +sys (3.4.2) +tibble (3.2.1) +tidyr (1.3.1) +tidyselect (1.2.0) +tinytex (0.49) +utf8 (1.2.4) +vctrs (0.6.5) +viridisLite (0.4.2) +withr (3.0.0) +xfun (0.42) +XML (3.99-0.16.1) +xml2 (1.3.6) +xtable (1.8-4) +XVector (0.42.0) +yaml (2.3.8) +zlibbioc (1.48.0) +zoo (1.8-12) diff --git a/revdep/checks.noindex/locuszoomr/old/locuszoomr.Rcheck/00check.log b/revdep/checks.noindex/locuszoomr/old/locuszoomr.Rcheck/00check.log new file mode 100644 index 0000000..746d813 --- /dev/null +++ b/revdep/checks.noindex/locuszoomr/old/locuszoomr.Rcheck/00check.log @@ -0,0 +1,20 @@ +* using log directory ‘/Users/myersta/Library/CloudStorage/OneDrive-NationalInstitutesofHealth/Rprojects_OneDrive/ldlinkr/revdep/checks.noindex/locuszoomr/old/locuszoomr.Rcheck’ +* using R version 4.3.2 (2023-10-31) +* using platform: x86_64-apple-darwin20 (64-bit) +* R was compiled by + Apple clang version 14.0.0 (clang-1400.0.29.202) + GNU Fortran (GCC) 12.2.0 +* running under: macOS Sonoma 14.3.1 +* using session charset: UTF-8 +* using options ‘--no-manual --no-build-vignettes’ +* checking for file ‘locuszoomr/DESCRIPTION’ ... OK +* this is package ‘locuszoomr’ version ‘0.2.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘cowplot’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR diff --git a/revdep/cran.md b/revdep/cran.md new file mode 100644 index 0000000..4b1b8a1 --- /dev/null +++ b/revdep/cran.md @@ -0,0 +1,7 @@ +## revdepcheck results + +We checked 2 reverse dependencies (1 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. + + * We saw 0 new problems + * We failed to check 0 packages + diff --git a/revdep/data.sqlite b/revdep/data.sqlite new file mode 100644 index 0000000..4efcb54 Binary files /dev/null and b/revdep/data.sqlite differ diff --git a/revdep/failures.md b/revdep/failures.md new file mode 100644 index 0000000..2af342e --- /dev/null +++ b/revdep/failures.md @@ -0,0 +1,85 @@ +# GRaNIE + +
+ +* Version: +* GitHub: https://github.com/CBIIT/LDlinkR +* Source code: NA +* Number of recursive dependencies: 0 + +
+ +## Error before installation + +### Devel + +``` + + There are binary versions available but the source versions are later: + binary source needs_compilation +digest 0.6.34 0.6.35 TRUE +tidyselect 1.2.0 1.2.1 TRUE + + Binaries will be installed + + +Error in download.file(url, destfile, method, mode = "wb", ...) : + cannot open URL 'https://cloud.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/abind_1.4-5.tgz' +In addition: Warning messages: +1: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://cloud.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/abind_1.4-5.tgz': status was 'SSL connect error' +2: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://cloud.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/abind_1.4-5.tgz': status was 'SSL connect error' +Warning in download.packages(pkgs, destdir = tmpd, available = available, : + download of package ‘abind’ failed +Warning in download.packages(pkgs, destdir = tmpd, available = available, : +... +2: In download.file(url, destfile, method, mode = "wb", ...) : + downloaded length 0 != reported length 0 +3: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn7_1.4.3.tar.gz': Timeout of 60 seconds was reached +4: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn7_1.4.3.tar.gz': Timeout of 60 seconds was reached +Warning in download.packages(pkgs, destdir = tmpd, available = available, : + download of package ‘BSgenome.Rnorvegicus.UCSC.rn7’ failed +Warning in download.packages(pkgs, destdir = tmpd, available = available, : + download of package ‘BSgenome.Rnorvegicus.UCSC.rn7’ failed + + +``` +### CRAN + +``` + + There are binary versions available but the source versions are later: + binary source needs_compilation +digest 0.6.34 0.6.35 TRUE +tidyselect 1.2.0 1.2.1 TRUE + + Binaries will be installed + + +Error in download.file(url, destfile, method, mode = "wb", ...) : + cannot open URL 'https://cloud.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/abind_1.4-5.tgz' +In addition: Warning messages: +1: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://cloud.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/abind_1.4-5.tgz': status was 'SSL connect error' +2: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://cloud.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/abind_1.4-5.tgz': status was 'SSL connect error' +Warning in download.packages(pkgs, destdir = tmpd, available = available, : + download of package ‘abind’ failed +Warning in download.packages(pkgs, destdir = tmpd, available = available, : +... +2: In download.file(url, destfile, method, mode = "wb", ...) : + downloaded length 0 != reported length 0 +3: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn7_1.4.3.tar.gz': Timeout of 60 seconds was reached +4: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn7_1.4.3.tar.gz': Timeout of 60 seconds was reached +Warning in download.packages(pkgs, destdir = tmpd, available = available, : + download of package ‘BSgenome.Rnorvegicus.UCSC.rn7’ failed +Warning in download.packages(pkgs, destdir = tmpd, available = available, : + download of package ‘BSgenome.Rnorvegicus.UCSC.rn7’ failed + + +``` diff --git a/revdep/library.noindex/LDlinkR/new/LDlinkR/CITATION b/revdep/library.noindex/LDlinkR/new/LDlinkR/CITATION new file mode 100644 index 0000000..4a91a5c --- /dev/null +++ b/revdep/library.noindex/LDlinkR/new/LDlinkR/CITATION @@ -0,0 +1,16 @@ +bibentry( + bibtype = "Article", + title = "LDlinkR: An R Package for Rapidly Calculating Linkage Disequilibrium Statistics in Diverse Populations", + author = c(as.person("Timothy A. Myers [aut]"), + as.person("Stephen J. Chanock [aut]"), + as.person("Mitchell J. Machiela [aut]")), + journal = "Frontiers in Genetics", + year = "2020", + volume = "11", + number = "157", + doi = "10.3389/fgene.2020.00157", + url = "https://www.frontiersin.org/articles/10.3389/fgene.2020.00157", + + header = "To cite LDlinkR in publications use:" + ) + diff --git a/revdep/library.noindex/LDlinkR/new/LDlinkR/DESCRIPTION b/revdep/library.noindex/LDlinkR/new/LDlinkR/DESCRIPTION new file mode 100644 index 0000000..f62de46 --- /dev/null +++ b/revdep/library.noindex/LDlinkR/new/LDlinkR/DESCRIPTION @@ -0,0 +1,45 @@ +Package: LDlinkR +Type: Package +Title: Calculating Linkage Disequilibrium (LD) in Human Population + Groups of Interest +Version: 1.3.0.9002 +Authors@R: + c(person(given = "Timothy A.", + family = "Myers", + role = c("aut", "cre"), + email = "myersta@mail.nih.gov", + comment = c(ORCID = "0000-0001-8127-3446")), + person(given = "Stephen J.", + family = "Chanock", + role = "aut", + email = "chanocks@mail.nih.gov"), + person(given = "Mitchell J.", + family = "Machiela", + role = "aut", + email = "mitchell.machiela@nih.gov", + comment = c(ORCID = "0000-0001-6538-9705"))) +Maintainer: Timothy A. Myers +Description: Provides access to the 'LDlink' API () + using the R console. This programmatic access facilitates researchers who are + interested in performing batch queries in 1000 Genomes Project (2015) + data using 'LDlink'. 'LDlink' is an interactive and powerful suite of web-based tools for querying + germline variants in human population groups of interest. For more details, please see + Machiela et al. (2015) . +License: GPL (>= 2) +URL: https://ldlink.nih.gov +BugReports: https://github.com/CBIIT/LDlinkR/issues +Encoding: UTF-8 +Imports: httr (>= 1.4.0), utils (>= 3.4.2) +Suggests: testthat, knitr, rmarkdown, spelling +VignetteBuilder: knitr +RoxygenNote: 7.3.1 +Language: en-US +RemoteType: local +RemoteUrl: + /Users/myersta/Library/CloudStorage/OneDrive-NationalInstitutesofHealth/Rprojects_OneDrive/ldlinkr +NeedsCompilation: no +Packaged: 2024-03-11 17:58:05 UTC; myersta +Author: Timothy A. Myers [aut, cre] (), + Stephen J. Chanock [aut], + Mitchell J. Machiela [aut] () +Built: R 4.3.2; ; 2024-03-11 17:58:06 UTC; unix diff --git a/revdep/library.noindex/LDlinkR/new/LDlinkR/INDEX b/revdep/library.noindex/LDlinkR/new/LDlinkR/INDEX new file mode 100644 index 0000000..2747f22 --- /dev/null +++ b/revdep/library.noindex/LDlinkR/new/LDlinkR/INDEX @@ -0,0 +1,34 @@ +LDexpress Determine if genomic variants are associated + with gene expression. +LDhap Calculates population specific haplotype + frequencies of all haplotypes observed for a + list of query variants. +LDmatrix Generates a data frame of pairwise linkage + disequilibrium statistics. +LDpair Investigates potentially correlated alleles for + a pair of variants. +LDpop Investigates allele frequencies and linkage + disequilibrium patterns across 1000 Genomes + Project populations. +LDproxy Explore proxy and putative functional variants + for a single query variant. +LDproxy_batch Query LDproxy using a list of query variants, + one per line. +LDtrait Determine if genomic variants are associated + with a trait or disease. +SNPchip Find commercial genotyping chip arrays for + variants of interest. +SNPclip Prune a list of variants by linkage + disequilibrium. +list_chips Provides a data frame listing the names and + abbreviation codes for available commercial SNP + Chip Arrays from Illumina and Affymetrix. +list_gtex_tissues Provides a data frame listing the GTEx full + names, 'LDexpress' full names (without spaces) + and acceptable abbreviation codes of the 54 + non-diseased tissue sites collected for the + GTEx Portal and used as input for the + 'LDexpress' function. +list_pop Provides a data frame listing the available + reference populations from the 1000 Genomes + Project. diff --git a/revdep/library.noindex/LDlinkR/new/LDlinkR/NAMESPACE b/revdep/library.noindex/LDlinkR/new/LDlinkR/NAMESPACE new file mode 100644 index 0000000..5b032a7 --- /dev/null +++ b/revdep/library.noindex/LDlinkR/new/LDlinkR/NAMESPACE @@ -0,0 +1,23 @@ +# Generated by roxygen2: do not edit by hand + +export(LDexpress) +export(LDhap) +export(LDmatrix) +export(LDpair) +export(LDpop) +export(LDproxy) +export(LDproxy_batch) +export(LDtrait) +export(SNPchip) +export(SNPclip) +export(list_chips) +export(list_gtex_tissues) +export(list_pop) +importFrom(httr,GET) +importFrom(httr,POST) +importFrom(httr,content) +importFrom(httr,http_error) +importFrom(httr,stop_for_status) +importFrom(utils,capture.output) +importFrom(utils,read.delim) +importFrom(utils,write.table) diff --git a/revdep/library.noindex/LDlinkR/new/LDlinkR/NEWS.md b/revdep/library.noindex/LDlinkR/new/LDlinkR/NEWS.md new file mode 100644 index 0000000..9325d7c --- /dev/null +++ b/revdep/library.noindex/LDlinkR/new/LDlinkR/NEWS.md @@ -0,0 +1,80 @@ +# LDlinkR 1.3.0.9002 (dev version) +* Added Zenodo DOI badge in version 1.3.0.9000 +* 3/1/2024 - Increased maximum allowed variants in LDmatrix to 2500 +* 3/1/2024 - Added bp window size parameter to LDproxy +* 3/4/2024 - Add bp window size parameter to LDproxy_batch +* 3/4/2024 - Test all changes +* 3/4/2024 - Update dev version number to 1.3.0.9002 +* 3/4/2024 - Update all package documentation and vignette with changes above +* 3/7/2024 - Merge branch ldproxy-bp-window with branch master + +# LDlinkR 1.3.0.9000 (development version) +* Add Zenodo DOI badge +* To do: Increase maximum allowed variants in LDmatrix to 3000. + +# LDlinkR 1.3.0 +* Change LDlink Domain URL to https://ldlink.nih.gov/ (previous url root will no longer work following an unspecified amount of time). +* Add Continuous Integration using Github Actions. +* Update citation file with bibentry style + +# LDlinkR 1.2.3 +* Add feature to provide root URL to API +* Fix bug that scrambled columns in LDproxy_batch when 'append' option is TRUE +* Update Roxygen version to 7.2.2 + +# LDlinkR 1.2.2 +* Issue #19, fix bug in LDtrait error handling of response data. +* Update CRAN downloads badge in README +* Remove link for 1000 Genomes Project in README and vignette + +# LDlinkR 1.2.1 +* Update version number +* Fix bug in LDexpress that returned GRCH37 results when genome build was GRCh38 or GRCh38 High Coverage. +* Fix bug in LDproxy handling of error/warning messages in response data. +* Update RoxygenNote to 7.2.0 + +# LDlinkR 1.2.0 +* Submission date: 2022-05-11 +* Issue #13 - Add new argument to `LDhap` (table_type) with four options for different types data output. +* Issue #14 - Fix `LDhap` valid input check for number of input 'snps', line 94. +* Add 'snps' to the WORDLIST +* Update test-ldhap with additional tests +* Update vignette with new `LDhap` usage examples with new argument. +* Make LDhap able to write to file for both types of data returned by the new 'table_type' options. +* Add feature 'genome_build' to support different genome builds, GRCh37(hg19), GRCh38(hg38), and GRCh38 High Coverage. +* Improve/update error and warning message returned in the response data from the LDlink API server. +* Fix CRAN note about 'LazyData' by removing line from Description file. +* Update README file. +* Add testthat tests for feature genome_build +* Add three new Illumina chips to SNPchip +* Add two new Affymetrix chips to SNPchip +* Major update to vignette with new feature genome_build + +# LDlinkR 1.1.2 +* Submission date: 2021-02-19 +* Add link to LDlink web site documentation. +* Correct code chunk in vignette FAQ #4, changed option to eval=FALSE; this vignette code chunk no longer requires an internet resource +* added notes to README and vignette that 'internet access required' to use +* Add code to check if required internet resources are available per CRAN + +# LDlinkR 1.1.1 +* Release date: 2021-02-02 +* Added three new functions, `LDtrait`, `LDexpress` & `list_gtex_tissues` +* Updated vignette with new descriptions of functions and examples. +* Major update to `README.md`, including basic examples +* Added a `NEWS.md` file to track changes to the package. +* Issue #2, fixed warning message from write.table in `LDproxy_batch` when append = TRUE +* Updated most function descriptions on package help page +* Added spell checking for building package + +# LDlinkR 1.0.2 +* Release date 2020-03-02 +* Minor updates + +# LDlinkR 1.0.1 +* Release date 2019-10-17 +* Minor updates made for publication. + +# LDlinkR 1.0.0 +* Release date 2019-08-01 +* Initial release. diff --git a/revdep/library.noindex/LDlinkR/new/LDlinkR/R/LDlinkR b/revdep/library.noindex/LDlinkR/new/LDlinkR/R/LDlinkR new file mode 100644 index 0000000..6686156 --- /dev/null +++ b/revdep/library.noindex/LDlinkR/new/LDlinkR/R/LDlinkR @@ -0,0 +1,27 @@ +# File share/R/nspackloader.R +# Part of the R package, https://www.R-project.org +# +# Copyright (C) 1995-2012 The R Core Team +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# A copy of the GNU General Public License is available at +# https://www.r-project.org/Licenses/ + +local({ + info <- loadingNamespaceInfo() + pkg <- info$pkgname + ns <- .getNamespace(as.name(pkg)) + if (is.null(ns)) + stop("cannot find namespace environment for ", pkg, domain = NA); + dbbase <- file.path(info$libname, pkg, "R", pkg) + lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.") +}) diff --git a/revdep/library.noindex/LDlinkR/new/LDlinkR/R/LDlinkR.rdb b/revdep/library.noindex/LDlinkR/new/LDlinkR/R/LDlinkR.rdb new file mode 100644 index 0000000..1fe32da Binary files /dev/null and b/revdep/library.noindex/LDlinkR/new/LDlinkR/R/LDlinkR.rdb differ diff --git a/revdep/library.noindex/LDlinkR/new/LDlinkR/R/LDlinkR.rdx b/revdep/library.noindex/LDlinkR/new/LDlinkR/R/LDlinkR.rdx new file mode 100644 index 0000000..7ce0c5b Binary files /dev/null and b/revdep/library.noindex/LDlinkR/new/LDlinkR/R/LDlinkR.rdx differ diff --git a/revdep/library.noindex/LDlinkR/new/LDlinkR/WORDLIST b/revdep/library.noindex/LDlinkR/new/LDlinkR/WORDLIST new file mode 100644 index 0000000..61a9731 --- /dev/null +++ b/revdep/library.noindex/LDlinkR/new/LDlinkR/WORDLIST @@ -0,0 +1,82 @@ +ADI +Affy +CEU +CMD +DOI +EBI +GRCH +GRCh +GTEx +GWAS +Github +HTTPS +Illumina +LD +LDassoc +LDexpress +LDhap +LDlink +LDlink's +LDmatrix +LDpair +LDpop +LDproxy +LDtrait +LazyData +MAF +METACRAN +NHGRI +OME +ORCID +Omentum +README +RefSNP +RefSeq +RegulomeDB +Roxygen +RoxygenNote +SNPchip +SNPclip +UCSC +VIS +WORDLIST +YRI +YourTokenHere +Zenodo +abc +al +allelic +basepairs +bibentry +bioinformatics +bp +btv +cM +chr +cis +dbSNP +dev +doi +eQTL +et +eval +germline +grch +gtex +hg +httr +indels +ldexpress +ldhap +ldlink +ldproxy +liftOver +metacran +nih +polymorphisms +programmatically +rsID +rsID's +snps +testthat +usethis diff --git a/revdep/library.noindex/LDlinkR/new/LDlinkR/help/AnIndex b/revdep/library.noindex/LDlinkR/new/LDlinkR/help/AnIndex new file mode 100644 index 0000000..d7c4050 --- /dev/null +++ b/revdep/library.noindex/LDlinkR/new/LDlinkR/help/AnIndex @@ -0,0 +1,15 @@ +LDlinkR-package LDlinkR-package +LDexpress LDexpress +LDhap LDhap +LDlinkR LDlinkR-package +LDmatrix LDmatrix +LDpair LDpair +LDpop LDpop +LDproxy LDproxy +LDproxy_batch LDproxy_batch +LDtrait LDtrait +list_chips list_chips +list_gtex_tissues list_gtex_tissues +list_pop list_pop +SNPchip SNPchip +SNPclip SNPclip diff --git a/revdep/library.noindex/LDlinkR/new/LDlinkR/help/LDlinkR.rdb b/revdep/library.noindex/LDlinkR/new/LDlinkR/help/LDlinkR.rdb new file mode 100644 index 0000000..a112901 Binary files /dev/null and b/revdep/library.noindex/LDlinkR/new/LDlinkR/help/LDlinkR.rdb differ diff --git a/revdep/library.noindex/LDlinkR/new/LDlinkR/help/LDlinkR.rdx b/revdep/library.noindex/LDlinkR/new/LDlinkR/help/LDlinkR.rdx new file mode 100644 index 0000000..5ed1cfe Binary files /dev/null and b/revdep/library.noindex/LDlinkR/new/LDlinkR/help/LDlinkR.rdx differ diff --git a/revdep/library.noindex/LDlinkR/new/LDlinkR/help/aliases.rds b/revdep/library.noindex/LDlinkR/new/LDlinkR/help/aliases.rds new file mode 100644 index 0000000..715a8a7 Binary files /dev/null and b/revdep/library.noindex/LDlinkR/new/LDlinkR/help/aliases.rds differ diff --git a/revdep/library.noindex/LDlinkR/new/LDlinkR/help/figures/logo.png b/revdep/library.noindex/LDlinkR/new/LDlinkR/help/figures/logo.png new file mode 100644 index 0000000..c60f90f Binary files /dev/null and b/revdep/library.noindex/LDlinkR/new/LDlinkR/help/figures/logo.png differ diff --git a/revdep/library.noindex/LDlinkR/new/LDlinkR/help/paths.rds b/revdep/library.noindex/LDlinkR/new/LDlinkR/help/paths.rds new file mode 100644 index 0000000..7ebbb68 Binary files /dev/null and b/revdep/library.noindex/LDlinkR/new/LDlinkR/help/paths.rds differ diff --git a/revdep/library.noindex/LDlinkR/new/LDlinkR/html/00Index.html b/revdep/library.noindex/LDlinkR/new/LDlinkR/html/00Index.html new file mode 100644 index 0000000..ccc5291 --- /dev/null +++ b/revdep/library.noindex/LDlinkR/new/LDlinkR/html/00Index.html @@ -0,0 +1,54 @@ + + +R: Calculating Linkage Disequilibrium (LD) in Human Population +Groups of Interest + + + +
+

Calculating Linkage Disequilibrium (LD) in Human Population +Groups of Interest + +

+
+
+[Up] +[Top] +

Documentation for package ‘LDlinkR’ version 1.3.0.9002

+ + + +

Help Pages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
LDexpressDetermine if genomic variants are associated with gene expression.
LDhapCalculates population specific haplotype frequencies of all haplotypes observed for a list of query variants.
LDmatrixGenerates a data frame of pairwise linkage disequilibrium statistics.
LDpairInvestigates potentially correlated alleles for a pair of variants.
LDpopInvestigates allele frequencies and linkage disequilibrium patterns across 1000 Genomes Project populations.
LDproxyExplore proxy and putative functional variants for a single query variant.
LDproxy_batchQuery LDproxy using a list of query variants, one per line.
LDtraitDetermine if genomic variants are associated with a trait or disease.
list_chipsProvides a data frame listing the names and abbreviation codes for available commercial SNP Chip Arrays from Illumina and Affymetrix.
list_gtex_tissuesProvides a data frame listing the GTEx full names, 'LDexpress' full names (without spaces) and acceptable abbreviation codes of the 54 non-diseased tissue sites collected for the GTEx Portal and used as input for the 'LDexpress' function.
list_popProvides a data frame listing the available reference populations from the 1000 Genomes Project.
SNPchipFind commercial genotyping chip arrays for variants of interest.
SNPclipPrune a list of variants by linkage disequilibrium.
+
diff --git a/revdep/library.noindex/LDlinkR/new/LDlinkR/html/R.css b/revdep/library.noindex/LDlinkR/new/LDlinkR/html/R.css new file mode 100644 index 0000000..c228909 --- /dev/null +++ b/revdep/library.noindex/LDlinkR/new/LDlinkR/html/R.css @@ -0,0 +1,130 @@ +@media screen { + .container { + padding-right: 10px; + padding-left: 10px; + margin-right: auto; + margin-left: auto; + max-width: 900px; + } +} + +.rimage img { /* from knitr - for examples and demos */ + width: 96%; + margin-left: 2%; +} + +.katex { font-size: 1.1em; } + +code { + color: inherit; + background: inherit; +} + +body { + line-height: 1.4; + background: white; + color: black; +} + +a:link { + background: white; + color: blue; +} + +a:visited { + background: white; + color: rgb(50%, 0%, 50%); +} + +h1 { + background: white; + color: rgb(55%, 55%, 55%); + font-family: monospace; + font-size: 1.4em; /* x-large; */ + text-align: center; +} + +h2 { + background: white; + color: rgb(40%, 40%, 40%); + font-family: monospace; + font-size: 1.2em; /* large; */ + text-align: center; +} + +h3 { + background: white; + color: rgb(40%, 40%, 40%); + font-family: monospace; + font-size: 1.2em; /* large; */ +} + +h4 { + background: white; + color: rgb(40%, 40%, 40%); + font-family: monospace; + font-style: italic; + font-size: 1.2em; /* large; */ +} + +h5 { + background: white; + color: rgb(40%, 40%, 40%); + font-family: monospace; +} + +h6 { + background: white; + color: rgb(40%, 40%, 40%); + font-family: monospace; + font-style: italic; +} + +img.toplogo { + width: 4em; + vertical-align: middle; +} + +img.arrow { + width: 30px; + height: 30px; + border: 0; +} + +span.acronym { + font-size: small; +} + +span.env { + font-family: monospace; +} + +span.file { + font-family: monospace; +} + +span.option{ + font-family: monospace; +} + +span.pkg { + font-weight: bold; +} + +span.samp{ + font-family: monospace; +} + +div.vignettes a:hover { + background: rgb(85%, 85%, 85%); +} + +tr { + vertical-align: top; +} + +span.rlang { + font-family: Courier New, Courier; + color: #666666; +} + diff --git a/revdep/library.noindex/LDlinkR/old/LDlinkR/CITATION b/revdep/library.noindex/LDlinkR/old/LDlinkR/CITATION new file mode 100644 index 0000000..4a91a5c --- /dev/null +++ b/revdep/library.noindex/LDlinkR/old/LDlinkR/CITATION @@ -0,0 +1,16 @@ +bibentry( + bibtype = "Article", + title = "LDlinkR: An R Package for Rapidly Calculating Linkage Disequilibrium Statistics in Diverse Populations", + author = c(as.person("Timothy A. Myers [aut]"), + as.person("Stephen J. Chanock [aut]"), + as.person("Mitchell J. Machiela [aut]")), + journal = "Frontiers in Genetics", + year = "2020", + volume = "11", + number = "157", + doi = "10.3389/fgene.2020.00157", + url = "https://www.frontiersin.org/articles/10.3389/fgene.2020.00157", + + header = "To cite LDlinkR in publications use:" + ) + diff --git a/revdep/library.noindex/LDlinkR/old/LDlinkR/DESCRIPTION b/revdep/library.noindex/LDlinkR/old/LDlinkR/DESCRIPTION new file mode 100644 index 0000000..7292f16 --- /dev/null +++ b/revdep/library.noindex/LDlinkR/old/LDlinkR/DESCRIPTION @@ -0,0 +1,44 @@ +Package: LDlinkR +Type: Package +Title: Calculating Linkage Disequilibrium (LD) in Human Population + Groups of Interest +Version: 1.3.0 +Authors@R: + c(person(given = "Timothy A.", + family = "Myers", + role = c("aut", "cre"), + email = "myersta@mail.nih.gov", + comment = c(ORCID = "0000-0001-8127-3446")), + person(given = "Stephen J.", + family = "Chanock", + role = "aut", + email = "chanocks@mail.nih.gov"), + person(given = "Mitchell J.", + family = "Machiela", + role = "aut", + email = "mitchell.machiela@nih.gov", + comment = c(ORCID = "0000-0001-6538-9705"))) +Maintainer: Timothy A. Myers +Description: Provides access to the 'LDlink' API () + using the R console. This programmatic access facilitates researchers who are + interested in performing batch queries in 1000 Genomes Project (2015) + data using 'LDlink'. 'LDlink' is an interactive and powerful suite of web-based tools for querying + germline variants in human population groups of interest. For more details, please see + Machiela et al. (2015) . +License: GPL (>= 2) +URL: https://ldlink.nih.gov +BugReports: https://github.com/CBIIT/LDlinkR/issues +Encoding: UTF-8 +Imports: httr (>= 1.4.0), utils (>= 3.4.2) +Suggests: testthat, knitr, rmarkdown, spelling +VignetteBuilder: knitr +RoxygenNote: 7.2.3 +Language: en-US +NeedsCompilation: no +Packaged: 2023-05-31 17:56:57 UTC; myersta +Author: Timothy A. Myers [aut, cre] (), + Stephen J. Chanock [aut], + Mitchell J. Machiela [aut] () +Repository: CRAN +Date/Publication: 2023-05-31 18:10:02 UTC +Built: R 4.3.0; ; 2023-05-31 20:41:52 UTC; unix diff --git a/revdep/library.noindex/LDlinkR/old/LDlinkR/INDEX b/revdep/library.noindex/LDlinkR/old/LDlinkR/INDEX new file mode 100644 index 0000000..2747f22 --- /dev/null +++ b/revdep/library.noindex/LDlinkR/old/LDlinkR/INDEX @@ -0,0 +1,34 @@ +LDexpress Determine if genomic variants are associated + with gene expression. +LDhap Calculates population specific haplotype + frequencies of all haplotypes observed for a + list of query variants. +LDmatrix Generates a data frame of pairwise linkage + disequilibrium statistics. +LDpair Investigates potentially correlated alleles for + a pair of variants. +LDpop Investigates allele frequencies and linkage + disequilibrium patterns across 1000 Genomes + Project populations. +LDproxy Explore proxy and putative functional variants + for a single query variant. +LDproxy_batch Query LDproxy using a list of query variants, + one per line. +LDtrait Determine if genomic variants are associated + with a trait or disease. +SNPchip Find commercial genotyping chip arrays for + variants of interest. +SNPclip Prune a list of variants by linkage + disequilibrium. +list_chips Provides a data frame listing the names and + abbreviation codes for available commercial SNP + Chip Arrays from Illumina and Affymetrix. +list_gtex_tissues Provides a data frame listing the GTEx full + names, 'LDexpress' full names (without spaces) + and acceptable abbreviation codes of the 54 + non-diseased tissue sites collected for the + GTEx Portal and used as input for the + 'LDexpress' function. +list_pop Provides a data frame listing the available + reference populations from the 1000 Genomes + Project. diff --git a/revdep/library.noindex/LDlinkR/old/LDlinkR/NAMESPACE b/revdep/library.noindex/LDlinkR/old/LDlinkR/NAMESPACE new file mode 100644 index 0000000..5b032a7 --- /dev/null +++ b/revdep/library.noindex/LDlinkR/old/LDlinkR/NAMESPACE @@ -0,0 +1,23 @@ +# Generated by roxygen2: do not edit by hand + +export(LDexpress) +export(LDhap) +export(LDmatrix) +export(LDpair) +export(LDpop) +export(LDproxy) +export(LDproxy_batch) +export(LDtrait) +export(SNPchip) +export(SNPclip) +export(list_chips) +export(list_gtex_tissues) +export(list_pop) +importFrom(httr,GET) +importFrom(httr,POST) +importFrom(httr,content) +importFrom(httr,http_error) +importFrom(httr,stop_for_status) +importFrom(utils,capture.output) +importFrom(utils,read.delim) +importFrom(utils,write.table) diff --git a/revdep/library.noindex/LDlinkR/old/LDlinkR/NEWS.md b/revdep/library.noindex/LDlinkR/old/LDlinkR/NEWS.md new file mode 100644 index 0000000..1730a55 --- /dev/null +++ b/revdep/library.noindex/LDlinkR/old/LDlinkR/NEWS.md @@ -0,0 +1,66 @@ +# LDlinkR 1.3.0 +* Change LDlink Domain URL to https://ldlink.nih.gov/ (previous url root will no longer work following an unspecified amount of time). +* Add Continuous Integration using Github Actions. +* Update citation file with bibentry style + +# LDlinkR 1.2.3 +* Add feature to provide root URL to API +* Fix bug that scrambled columns in LDproxy_batch when 'append' option is TRUE +* Update Roxygen version to 7.2.2 + +# LDlinkR 1.2.2 +* Issue #19, fix bug in LDtrait error handling of response data. +* Update CRAN downloads badge in README +* Remove link for 1000 Genomes Project in README and vignette + +# LDlinkR 1.2.1 +* Update version number +* Fix bug in LDexpress that returned GRCH37 results when genome build was GRCh38 or GRCh38 High Coverage. +* Fix bug in LDproxy handling of error/warning messages in response data. +* Update RoxygenNote to 7.2.0 + +# LDlinkR 1.2.0 +* Submission date: 2022-05-11 +* Issue #13 - Add new argument to `LDhap` (table_type) with four options for different types data output. +* Issue #14 - Fix `LDhap` valid input check for number of input 'snps', line 94. +* Add 'snps' to the WORDLIST +* Update test-ldhap with additional tests +* Update vignette with new `LDhap` usage examples with new argument. +* Make LDhap able to write to file for both types of data returned by the new 'table_type' options. +* Add feature 'genome_build' to support different genome builds, GRCh37(hg19), GRCh38(hg38), and GRCh38 High Coverage. +* Improve/update error and warning message returned in the response data from the LDlink API server. +* Fix CRAN note about 'LazyData' by removing line from Description file. +* Update README file. +* Add testthat tests for feature genome_build +* Add three new Illumina chips to SNPchip +* Add two new Affymetrix chips to SNPchip +* Major update to vignette with new feature genome_build + +# LDlinkR 1.1.2 +* Submission date: 2021-02-19 +* Add link to LDlink web site documentation. +* Correct code chunk in vignette FAQ #4, changed option to eval=FALSE; this vignette code chunk no longer requires an internet resource +* added notes to README and vignette that 'internet access required' to use +* Add code to check if required internet resources are available per CRAN + +# LDlinkR 1.1.1 +* Release date: 2021-02-02 +* Added three new functions, `LDtrait`, `LDexpress` & `list_gtex_tissues` +* Updated vignette with new descriptions of functions and examples. +* Major update to `README.md`, including basic examples +* Added a `NEWS.md` file to track changes to the package. +* Issue #2, fixed warning message from write.table in `LDproxy_batch` when append = TRUE +* Updated most function descriptions on package help page +* Added spell checking for building package + +# LDlinkR 1.0.2 +* Release date 2020-03-02 +* Minor updates + +# LDlinkR 1.0.1 +* Release date 2019-10-17 +* Minor updates made for publication. + +# LDlinkR 1.0.0 +* Release date 2019-08-01 +* Initial release. diff --git a/revdep/library.noindex/LDlinkR/old/LDlinkR/R/LDlinkR b/revdep/library.noindex/LDlinkR/old/LDlinkR/R/LDlinkR new file mode 100644 index 0000000..6686156 --- /dev/null +++ b/revdep/library.noindex/LDlinkR/old/LDlinkR/R/LDlinkR @@ -0,0 +1,27 @@ +# File share/R/nspackloader.R +# Part of the R package, https://www.R-project.org +# +# Copyright (C) 1995-2012 The R Core Team +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# A copy of the GNU General Public License is available at +# https://www.r-project.org/Licenses/ + +local({ + info <- loadingNamespaceInfo() + pkg <- info$pkgname + ns <- .getNamespace(as.name(pkg)) + if (is.null(ns)) + stop("cannot find namespace environment for ", pkg, domain = NA); + dbbase <- file.path(info$libname, pkg, "R", pkg) + lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.") +}) diff --git a/revdep/library.noindex/LDlinkR/old/LDlinkR/R/LDlinkR.rdb b/revdep/library.noindex/LDlinkR/old/LDlinkR/R/LDlinkR.rdb new file mode 100644 index 0000000..68e3e04 Binary files /dev/null and b/revdep/library.noindex/LDlinkR/old/LDlinkR/R/LDlinkR.rdb differ diff --git a/revdep/library.noindex/LDlinkR/old/LDlinkR/R/LDlinkR.rdx b/revdep/library.noindex/LDlinkR/old/LDlinkR/R/LDlinkR.rdx new file mode 100644 index 0000000..7cc75c4 Binary files /dev/null and b/revdep/library.noindex/LDlinkR/old/LDlinkR/R/LDlinkR.rdx differ diff --git a/revdep/library.noindex/LDlinkR/old/LDlinkR/WORDLIST b/revdep/library.noindex/LDlinkR/old/LDlinkR/WORDLIST new file mode 100644 index 0000000..a36ec81 --- /dev/null +++ b/revdep/library.noindex/LDlinkR/old/LDlinkR/WORDLIST @@ -0,0 +1,78 @@ +ADI +Affy +CEU +CMD +EBI +GRCH +GRCh +GTEx +GWAS +Github +HTTPS +Illumina +LD +LDassoc +LDexpress +LDhap +LDlink +LDlink's +LDmatrix +LDpair +LDpop +LDproxy +LDtrait +LazyData +MAF +METACRAN +NHGRI +OME +ORCID +Omentum +README +RefSNP +RefSeq +RegulomeDB +Roxygen +RoxygenNote +SNPchip +SNPclip +UCSC +VIS +WORDLIST +YRI +YourTokenHere +abc +al +allelic +basepairs +bibentry +bioinformatics +bp +btv +cM +chr +cis +dbSNP +doi +eQTL +et +eval +germline +grch +gtex +hg +httr +indels +ldexpress +ldhap +ldlink +liftOver +metacran +nih +polymorphisms +programmatically +rsID +rsID's +snps +testthat +usethis diff --git a/revdep/library.noindex/LDlinkR/old/LDlinkR/help/AnIndex b/revdep/library.noindex/LDlinkR/old/LDlinkR/help/AnIndex new file mode 100644 index 0000000..d7c4050 --- /dev/null +++ b/revdep/library.noindex/LDlinkR/old/LDlinkR/help/AnIndex @@ -0,0 +1,15 @@ +LDlinkR-package LDlinkR-package +LDexpress LDexpress +LDhap LDhap +LDlinkR LDlinkR-package +LDmatrix LDmatrix +LDpair LDpair +LDpop LDpop +LDproxy LDproxy +LDproxy_batch LDproxy_batch +LDtrait LDtrait +list_chips list_chips +list_gtex_tissues list_gtex_tissues +list_pop list_pop +SNPchip SNPchip +SNPclip SNPclip diff --git a/revdep/library.noindex/LDlinkR/old/LDlinkR/help/LDlinkR.rdb b/revdep/library.noindex/LDlinkR/old/LDlinkR/help/LDlinkR.rdb new file mode 100644 index 0000000..2464ecb Binary files /dev/null and b/revdep/library.noindex/LDlinkR/old/LDlinkR/help/LDlinkR.rdb differ diff --git a/revdep/library.noindex/LDlinkR/old/LDlinkR/help/LDlinkR.rdx b/revdep/library.noindex/LDlinkR/old/LDlinkR/help/LDlinkR.rdx new file mode 100644 index 0000000..10ffa00 Binary files /dev/null and b/revdep/library.noindex/LDlinkR/old/LDlinkR/help/LDlinkR.rdx differ diff --git a/revdep/library.noindex/LDlinkR/old/LDlinkR/help/aliases.rds b/revdep/library.noindex/LDlinkR/old/LDlinkR/help/aliases.rds new file mode 100644 index 0000000..c543b56 Binary files /dev/null and b/revdep/library.noindex/LDlinkR/old/LDlinkR/help/aliases.rds differ diff --git a/revdep/library.noindex/LDlinkR/old/LDlinkR/help/figures/logo.png b/revdep/library.noindex/LDlinkR/old/LDlinkR/help/figures/logo.png new file mode 100644 index 0000000..c60f90f Binary files /dev/null and b/revdep/library.noindex/LDlinkR/old/LDlinkR/help/figures/logo.png differ diff --git a/revdep/library.noindex/LDlinkR/old/LDlinkR/help/paths.rds b/revdep/library.noindex/LDlinkR/old/LDlinkR/help/paths.rds new file mode 100644 index 0000000..464353d Binary files /dev/null and b/revdep/library.noindex/LDlinkR/old/LDlinkR/help/paths.rds differ diff --git a/revdep/library.noindex/LDlinkR/old/LDlinkR/html/00Index.html b/revdep/library.noindex/LDlinkR/old/LDlinkR/html/00Index.html new file mode 100644 index 0000000..1963454 --- /dev/null +++ b/revdep/library.noindex/LDlinkR/old/LDlinkR/html/00Index.html @@ -0,0 +1,55 @@ + + +R: Calculating Linkage Disequilibrium (LD) in Human Population +Groups of Interest + + + +
+

Calculating Linkage Disequilibrium (LD) in Human Population +Groups of Interest + +

+
+
+[Up] +[Top] +

Documentation for package ‘LDlinkR’ version 1.3.0

+ + + +

Help Pages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
LDexpressDetermine if genomic variants are associated with gene expression.
LDhapCalculates population specific haplotype frequencies of all haplotypes observed for a list of query variants.
LDmatrixGenerates a data frame of pairwise linkage disequilibrium statistics.
LDpairInvestigates potentially correlated alleles for a pair of variants.
LDpopInvestigates allele frequencies and linkage disequilibrium patterns across 1000 Genomes Project populations.
LDproxyExplore proxy and putative functional variants for a single query variant.
LDproxy_batchQuery LDproxy using a list of query variants, one per line.
LDtraitDetermine if genomic variants are associated with a trait or disease.
list_chipsProvides a data frame listing the names and abbreviation codes for available commercial SNP Chip Arrays from Illumina and Affymetrix.
list_gtex_tissuesProvides a data frame listing the GTEx full names, 'LDexpress' full names (without spaces) and acceptable abbreviation codes of the 54 non-diseased tissue sites collected for the GTEx Portal and used as input for the 'LDexpress' function.
list_popProvides a data frame listing the available reference populations from the 1000 Genomes Project.
SNPchipFind commercial genotyping chip arrays for variants of interest.
SNPclipPrune a list of variants by linkage disequilibrium.
+
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