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BiocCheck: REQUIRED count: 1 RECOMMENDED count: 1 CONSIDERATION count:6 #44

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BiocCheck: REQUIRED count: 1 RECOMMENDED count: 1 CONSIDERATION count:6 #44

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13 changes: 10 additions & 3 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
Package: arkas
Type: Package
Title: A package that complements Kallisto for quick, informative *seq analysis
Version: 0.44.9
Date: 2016-08-13
Version: 0.98.0
Date: 2016-08-26
Author: Tim Triche, Jr., Anthony Colombo, Harold Pimentel
biocViews: RNASeq, Transcriptomics
Depends:
SummarizedExperiment,
tools
Expand All @@ -28,7 +29,13 @@ Imports:
GenomeInfoDb,
methods,
S4Vectors,
GenomicFeatures
GenomicFeatures,
grDevices,
graphics,
grid,
parallel,
stats,
utils
Suggests:
knitr,
roxygen2,
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2 changes: 2 additions & 0 deletions NAMESPACE
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Expand Up @@ -64,6 +64,8 @@ importFrom(IRanges,reduce)
importFrom(RUVSeq,RUVg)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(TxDbLite,createAnnotationPackage)
importFrom(TxDbLite,findDupes)
importFrom(TxDbLite,getAnnotationType)
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2 changes: 2 additions & 0 deletions R/collapseByTss.R
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Expand Up @@ -7,6 +7,8 @@
#' @return the TSS for transcripts on chr1:22/X/Y/M to collapse by TSS,
#' or NA for transcripts originating anywhere else (ERCC, repeats, &c)
#'
#' @importFrom S4Vectors queryHits
#' @importFrom S4Vectors subjectHits
#' @importFrom GenomeInfoDb seqlevels
#' @importFrom GenomeInfoDb seqlevelsStyle
#' @importFrom GenomeInfoDb seqlevelsInGroup seqnames
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2 changes: 1 addition & 1 deletion R/extractIndexName.R
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Expand Up @@ -8,6 +8,6 @@
extractIndexName <- function(callinfo) {
pop <- function(x) x[length(x)]
popsplit <- function(x, y=.Platform$file.sep) pop(strsplit(x, y)[[1]])
tokens <- strsplit(callinfo, " ", fixed=T)[[1]]
tokens <- strsplit(callinfo, " ", fixed=TRUE)[[1]]
popsplit(tokens[grep("^-i$", tokens) + 1])
}