diff --git a/DESCRIPTION b/DESCRIPTION index 30f8399..eb911aa 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -16,17 +16,17 @@ Authors@R: c( role = "aut", comment = c(ORCID = "0000-0003-0173-4324"))) Description: Standardize the pre-processing of genomic variants before - performing a bacterial genome-wide association study (bGWAS). prewas creates - a variant matrix (where each row is a variant, each column is a sample, and - the entries are presence - 1 - or absence - 0 - of the variant) that can be - used as input for bGWAS tools. When creating the binary variant matrix, - prewas can perform 3 pre-processing steps including: dealing with + performing a bacterial genome-wide association study (bGWAS). 'prewas' + creates a variant matrix (where each row is a variant, each column is a + sample, and the entries are presence - 1 - or absence - 0 - of the variant) + that can be used as input for bGWAS tools. When creating the binary variant + matrix, 'prewas' can perform 3 pre-processing steps including: dealing with multiallelic SNPs, (optional) dealing with SNPs in overlapping genes, and - choosing a reference allele. prewas can output matrices for use with both + choosing a reference allele. 'prewas' can output matrices for use with both SNP-based bGWAS and gene-based bGWAS. This method is described in Saund et - al. (2020) . prewas can also provide - gene matrices for variants with specific SnpEff annotations (Cingolani et - al. 2012). + al. (2020) . 'prewas' can also provide + gene matrices for variants with specific annotations from the 'SnpEff' + software (Cingolani et al. 2012). URL: https://github.com/Snitkin-Lab-Umich/prewas BugReports: https://github.com/Snitkin-Lab-Umich/prewas/issues License: MIT + file LICENSE @@ -48,4 +48,4 @@ Suggests: knitr (>= 1.24), rmarkdown (>= 1.15) VignetteBuilder: knitr -Date: 2021-03-24 +Date: 2021-04-01 diff --git a/cran-comments.md b/cran-comments.md index f8b6378..c02b3e7 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,8 +1,8 @@ ## Resubmission -* Updated URLs to start with https instead of http in DESCRIPTION and README.md -* Fixed DOI format in DESCRIPTION -* Updated package version number in DESCRIPTION +* Placed package names and software names in single quotes in DESCRIPTION +* Updated CITATION with current journal article information +* Explained that the word 'SnpEff' in the descriptoin text is not an acronym, but the name of a piece of software ## Package update Prewas was archived from CRAN on 2020-07-05 because a dependency, vcfR, was archived on CRAN. Since then vcfR has been updated on CRAN and so prewas will now be able to install successfully. @@ -21,7 +21,7 @@ No errors, warnings, or notes. NOTE: ``` Possibly mis-spelled words in DESCRIPTION: - Cingolani (29:66) + Cingolani (29:66) Pre (3:13) Saund (27:71) SnpEff (29:46) @@ -33,4 +33,4 @@ Possibly mis-spelled words in DESCRIPTION: prewas (20:67, 24:5, 26:34, 28:57) ``` -The NOTE is spurious because these words are all correctly spelled technical terms, Latin, or last names. +The NOTE is spurious because these words are all correctly spelled technical terms (bGWAS, multiallelic), Latin (et al), software (SnpEff, prewas), or last names (Cingolani, Saund). diff --git a/inst/CITATION b/inst/CITATION index aebcc4b..f6a4183 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -2,14 +2,16 @@ citHeader("To cite prewas in publications use:") citEntry( entry = "article", - title = "prewas:Data pre-processing for more informative bacterial GWAS", + title = "prewas: data pre-processing for more informative bacterial GWAS", author = as.person("Katie Saund* [aut], Zena Lapp* [aut], Stephanie N. Thiede* [aut], Ali Pirani [aut], and Evan S. Snitkin [aut]"), - journal = "bioRxiv", - year = "2019", + journal = "Microbial Genomics", + year = "2020", + volume = "6", + number = "5", textVersion = paste( - "prewas: Data pre-processing for more informative bacterial GWAS", + "prewas: data pre-processing for more informative bacterial GWAS", "Katie Saund*, Zena Lapp*, Stephanie N. Thiede*, Ali Pirani, Evan S Snitkin", - "bioRxiv 2019.12.20.873158; doi: https://doi.org/10.1101/2019.12.20.873158" + "Microbial Genomics 2020 doi:10.1099/mgen.0.000368" ) )