git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@98136 bc3139a8-67e5-0310-9ffc-ced21a209358
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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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@@ -18,10 +18,6 @@ toy_reads_sam <- function() |
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|
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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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@@ -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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|
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\begin{document} |
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|
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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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|
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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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|
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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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|
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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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|
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<<ScanBamParam>>= |
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flag0 <- scanBamFlag(isSecondaryAlignment=FALSE, |