Interval statistics
-December 21 2024
+December 27 2024
Source:vignettes/interval-stats.Rmd
interval-stats.Rmdvalr overview
-2024-12-21
+2024-12-27
Source:vignettes/valr.Rmd
valr.RmdDevelopers
Dev status
-
+
valr (development version)
-read_bigwig()andread_gtf()were deprecated as rtracklayer is no longer avilable on CRAN.
+read_bigwig()andread_gtf()were deprecated. The rtracklayer package used for this functionality is no longer a dependency of valr due to errors from CRAN AddressSantizer checks of the UCSC c-library code vendored in rtracklayer.valr now depends on R >= 4.0.0.
diff --git a/dev/pkgdown.yml b/dev/pkgdown.yml
index 3d8a6787..8deb2903 100644
--- a/dev/pkgdown.yml
+++ b/dev/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: 5c03b7444923f7c797b8b283e175f8eed63797a7
articles:
interval-stats: interval-stats.html
valr: valr.html
-last_built: 2024-12-21T14:19Z
+last_built: 2024-12-27T15:34Z
urls:
reference: https://rnabioco.github.io/valr/reference
article: https://rnabioco.github.io/valr/articles
diff --git a/dev/search.json b/dev/search.json
index 999cfc36..bd046759 100644
--- a/dev/search.json
+++ b/dev/search.json
@@ -1 +1 @@
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Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://rnabioco.github.io/valr/dev/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://rnabioco.github.io/valr/dev/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://rnabioco.github.io/valr/dev/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://rnabioco.github.io/valr/dev/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://rnabioco.github.io/valr/dev/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://rnabioco.github.io/valr/dev/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://rnabioco.github.io/valr/dev/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://rnabioco.github.io/valr/dev/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.0, available https://www.contributor-covenant.org/version/2/0/ code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https:// www.contributor-covenant.org/translations.","code":""},{"path":"https://rnabioco.github.io/valr/dev/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contributing to valr","title":"Contributing to valr","text":"outlines propose change valr. detailed info contributing , tidyverse packages, please see development contributing guide.","code":""},{"path":"https://rnabioco.github.io/valr/dev/CONTRIBUTING.html","id":"fixing-typos","dir":"","previous_headings":"","what":"Fixing typos","title":"Contributing to valr","text":"can fix typos, spelling mistakes, grammatical errors documentation directly using GitHub web interface, long changes made source file. generally means ’ll need edit roxygen2 comments .R, .Rd file. can find .R file generates .Rd reading comment first line.","code":""},{"path":"https://rnabioco.github.io/valr/dev/CONTRIBUTING.html","id":"bigger-changes","dir":"","previous_headings":"","what":"Bigger changes","title":"Contributing to valr","text":"want make bigger change, ’s good idea first file issue make sure someone team agrees ’s needed. ’ve found bug, please file issue illustrates bug minimal reprex (also help write unit test, needed).","code":""},{"path":"https://rnabioco.github.io/valr/dev/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"Bigger changes","what":"Pull request process","title":"Contributing to valr","text":"Fork package clone onto computer. haven’t done , recommend using usethis::create_from_github(\"rnabioco/valr\", fork = TRUE). Install development dependences devtools::install_dev_deps(), make sure package passes R CMD check running devtools::check(). R CMD check doesn’t pass cleanly, ’s good idea ask help continuing. Create Git branch pull request (PR). recommend using usethis::pr_init(\"brief-description--change\"). Make changes, commit git, create PR running usethis::pr_push(), following prompts browser. title PR briefly describe change. body PR contain Fixes #issue-number. user-facing changes, add bullet top NEWS.md (.e. just first header). Follow style described https://style.tidyverse.org/news.html.","code":""},{"path":"https://rnabioco.github.io/valr/dev/CONTRIBUTING.html","id":"code-style","dir":"","previous_headings":"Bigger changes","what":"Code style","title":"Contributing to valr","text":"New code follow tidyverse style guide. can use styler package apply styles, please don’t restyle code nothing PR. use roxygen2, Markdown syntax, documentation. use testthat unit tests. Contributions test cases included easier accept.","code":""},{"path":"https://rnabioco.github.io/valr/dev/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contributing to valr","text":"Please note valr project released Contributor Code Conduct. contributing project agree abide terms.","code":""},{"path":"https://rnabioco.github.io/valr/dev/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2016-2018 Jay R Hesselberth Kent Riemondy Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://rnabioco.github.io/valr/dev/articles/interval-stats.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Interval statistics","text":"valr includes several functions exploring statistical relationships sets intervals. Calculate significance overlaps sets intervals bed_fisher() bed_projection(). Quantify relative absolute distances sets intervals bed_reldist() bed_absdist(). Quantify extent overlap sets intervals bed_jaccard(). vignette explore relationship transcription start sites repetitive elements human genome.","code":"library(valr) #> Error in get(paste0(generic, \".\", class), envir = get_method_env()) : #> object 'type_sum.accel' not found library(dplyr) library(ggplot2) library(cowplot) library(tidyr) # load repeats and genes. Data in the valr package is restricted to chr22; the entire # files can be downloaded from UCSC. rpts <- read_bed(valr_example(\"hg19.rmsk.chr22.bed.gz\")) genes <- read_bed12(valr_example(\"hg19.refGene.chr22.bed.gz\")) # load chrom sizes genome <- read_genome(valr_example(\"hg19.chrom.sizes.gz\")) # create 1 bp intervals representing transcription start sites tss <- create_tss(genes) tss #> # A tibble: 1,267 × 6 #> chrom start end name score strand #> #> 1 chr22 16193008 16193009 NR_122113 0 - #> 2 chr22 16157078 16157079 NR_133911 0 + #> 3 chr22 16162065 16162066 NR_073459 0 + #> 4 chr22 16162065 16162066 NR_073460 0 + #> 5 chr22 16231288 16231289 NR_132385 0 - #> 6 chr22 16287936 16287937 NM_001136213 0 - #> 7 chr22 16274608 16274609 NR_046571 0 + #> 8 chr22 16449803 16449804 NM_001005239 0 - #> 9 chr22 17073699 17073700 NM_014406 0 - #> 10 chr22 17082800 17082801 NR_001591 0 + #> # ℹ 1,257 more rows"},{"path":"https://rnabioco.github.io/valr/dev/articles/interval-stats.html","id":"distance-metrics","dir":"Articles","previous_headings":"","what":"Distance metrics","title":"Interval statistics","text":"First define function takes x y intervals computes distance statistics (using bed_reldist() bed_absdist()) specified groups. value statistic assigned .value column. use distance_stats() function apply bed_absdist() function group data. done set shuffled group data. bed_shuffle() used shuffle coordinates repeats within chromosome (.e., coordinates change, chromosome stays .) Now can bind observed shuffled data together, tidying put data format appropriate statistical test. involves: unnest()ing data frames creating groups repeat (name), stat (reldist absdist) type (obs shf) adding unique surrogate row numbers group using tidyr::pivot_wider() create two new obs shuf columns removing rows NA values. Now data formatted, can use non-parametric ks.test() determine whether significant differences observed shuffled data group. broom::tidy() used reformat results test tibble, results test pivoted type column test type. Histgrams different stats help visualize distribution p.values. can also assess false discovery rates (q.values) using p.adjust(). Finally can visualize results using stat_ecdf().","code":"distance_stats <- function(x, y, genome, group_var, type = NA) { group_by(x, !!rlang::sym(group_var)) |> do( reldist = bed_reldist(., y, detail = TRUE) |> select(.value = .reldist), absdist = bed_absdist(., y, genome) |> select(.value = .absdist) ) |> tidyr::pivot_longer( cols = -name, names_to = \"stat\", values_to = \"value\" ) |> mutate(type = type) } obs_stats <- distance_stats(rpts, tss, genome, \"name\", \"obs\") obs_stats #> # A tibble: 2,106 × 4 #> name stat value type #>