Browse code

Rsamtools is now required instead of suggested only

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@98136 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 07/01/2015 20:07:56
Showing 8 changed files

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@@ -1,7 +1,7 @@
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 Package: SplicingGraphs
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 Title: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads
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 	to them
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-Version: 1.7.3
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+Version: 1.7.4
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 Author: D. Bindreither, M. Carlson, M. Morgan, H. Pages
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 License: Artistic-2.0
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 Description: This package allows the user to create, manipulate, and visualize
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@@ -14,8 +14,8 @@ Depends: GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22),
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 	 Rgraphviz (>= 2.3.7)
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 Imports: methods, utils, igraph,
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 	 BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges,
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-	 GenomicFeatures, GenomicAlignments, graph, Rgraphviz
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-Suggests: igraph, Gviz, Rsamtools (>= 1.19.17),
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+	 GenomicFeatures, Rsamtools, GenomicAlignments, graph, Rgraphviz
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+Suggests: igraph, Gviz,
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 	 TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14,
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 	 RUnit
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 Collate: utils.R
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@@ -11,6 +11,7 @@ import(IRanges)
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 import(GenomeInfoDb)
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 import(GenomicRanges)
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 import(GenomicFeatures)
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+importFrom(Rsamtools, asBam)
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 import(GenomicAlignments)
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 importFrom(graph, nodeDataDefaults, nodeData,
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@@ -18,10 +18,6 @@ toy_reads_sam <- function()
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 toy_reads_bam <- function()
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 {
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-    ## The Rsamtools package is needed for asBam().
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-    if (!requireNamespace("Rsamtools", quietly=TRUE))
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-        stop("Couldn't load the Rsamtools package. Please install ",
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-             "the Rsamtools\n  package and try again.")
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     toy_reads_bam <- try(get("toy_reads_bam", envir=.toy_reads_bam_cache,
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                              inherits=FALSE), silent=TRUE)
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     if (!is(toy_reads_bam, "try-error"))
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@@ -13,7 +13,6 @@
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 .load_toy_reads <- function()
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 {
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-    library(Rsamtools)
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     flag0 <- scanBamFlag(isSecondaryAlignment=FALSE,
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                          isNotPassingQualityControls=FALSE,
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                          isDuplicate=FALSE)
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@@ -37,6 +37,8 @@
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 }
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 \usage{
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+## Constructor:
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+
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 SplicingGraphs(x, grouping=NULL, min.ntx=2, max.ntx=NA, check.introns=TRUE)
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 ## SplicingGraphs basic API:
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@@ -75,7 +75,6 @@ removeReads(sg)
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   when preparing the \link[Rsamtools]{ScanBamParam} object used to load
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   the reads. For example:
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   \preformatted{
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-    library(Rsamtools)
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     flag0 <- scanBamFlag(isSecondaryAlignment=FALSE,
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                          isNotPassingQualityControls=FALSE,
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                          isDuplicate=FALSE)
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@@ -143,7 +142,6 @@ names(sg)
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 ## alignments, reads not passing quality controls, and PCR or optical
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 ## duplicates (see ?scanBamFlag in the Rsamtools package for more
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 ## information):
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-library(Rsamtools)
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 flag0 <- scanBamFlag(isSecondaryAlignment=FALSE,
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                      isNotPassingQualityControls=FALSE,
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                      isDuplicate=FALSE)
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@@ -145,7 +145,6 @@ plot(sgraph(sg["geneD"], tx_id.as.edge.label=TRUE, as.igraph=TRUE))
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 ## secondary alignments, reads not passing quality controls, and PCR or
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 ## optical duplicates (see ?scanBamFlag in the Rsamtools package for
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 ## more information):
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-library(Rsamtools)
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 flag0 <- scanBamFlag(isSecondaryAlignment=FALSE,
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                      isNotPassingQualityControls=FALSE,
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                      isDuplicate=FALSE)
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@@ -1,5 +1,5 @@
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 %\VignetteIndexEntry{Splicing graphs and RNA-seq data}
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-%\VignetteDepends{SplicingGraphs,TxDb.Hsapiens.UCSC.hg19.knownGene,RNAseqData.HNRNPC.bam.chr14,Rsamtools,GenomicAlignments,Gviz}
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+%\VignetteDepends{SplicingGraphs,TxDb.Hsapiens.UCSC.hg19.knownGene,RNAseqData.HNRNPC.bam.chr14,Gviz}
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 %\VignetteKeywords{Annotation}
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 %\VignettePackage{SplicingGraphs}
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 \documentclass{article}
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@@ -39,7 +39,7 @@
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   Marc Carlson\and
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   Martin Morgan}
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-\date{Last modified: July 2014; Compiled: \today}
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+\date{Last modified: January 2015; Compiled: \today}
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 \begin{document}
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@@ -822,7 +822,6 @@ single- or paired-end. This can be checked with the
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 package:
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 <<quickBamFlagSummary>>=
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-library(Rsamtools)
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 quickBamFlagSummary(bam_files[1], main.groups.only=TRUE)
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 @
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@@ -833,7 +832,6 @@ package. As a quick example, we load the reads located on the first 20
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 million bases of chromosome 14:
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 <<readGAlignmentPairs>>=
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-library(GenomicAlignments)
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 param <- ScanBamParam(which=GRanges("chr14", IRanges(1, 20000000)))
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 galp <- readGAlignmentPairs(bam_files[1], param=param)
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 length(galp)  # nb of alignment pairs
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@@ -862,8 +860,8 @@ at a time. When we load the files, we want to filter out secondary
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 alignments, reads not passing quality controls, and PCR or optical
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 duplicates. This is done by preparing a \Rclass{ScanBamParam} object
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 that we'll pass to \Rfunction{readGAlignmentPairs} (see
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-\Rfunction{ScanBamParam} in the Rsamtools package for more information
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-about this):
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+\Rfunction{ScanBamParam} in the \Rpackage{Rsamtools} package for more
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+information about this):
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 <<ScanBamParam>>=
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 flag0 <- scanBamFlag(isSecondaryAlignment=FALSE,