Update citation to MGen paper. Update cran-comments with fixes reques…

…ted by CRAN admin. Make changes to DESCRIPTION as requested by CRAN admin.
Snitkin-Lab-Umich · Apr 1, 2021 · b0cff65 · b0cff65
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diff --git 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) <doi:10.1099/mgen.0.000368>. prewas can also provide 
-    gene matrices for variants with specific SnpEff annotations (Cingolani et 
-    al. 2012).
+    al. (2020) <doi:10.1099/mgen.0.000368>. '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
@@ -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
@@ -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"
   )
 )