git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@59179 bc3139a8-67e5-0310-9ffc-ced21a209358
Daniel Jones authored on 13/10/2011 18:02:34
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@@ -1,5 +1,5 @@ |
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Package: seqbias |
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-Version: 1.1.3 |
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+Version: 1.1.4 |
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Date: 25-12-2010 |
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Title: Estimation of per-position bias in high-throughput sequencing data |
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Description: This package implements a model of per-position sequencing bias in |
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@@ -11,6 +11,7 @@ Maintainer: Daniel Jones <dcjones@cs.washington.edu> |
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Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0), |
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Biostrings (>= 2.15.0), methods |
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LinkingTo: Rsamtools |
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+Imports: zlibbioc |
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biocViews: Sequencing, HighThroughputSequencing |
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LazyLoad: yes |
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License: LGPL-3 |
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\title{Counting reads across intervals}
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\description{Counts the number of reads starting at each position across given
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genomic intervals} |
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-\usage{count.reads(reads_fn, I, sb=NULL, binary=FALSE, sum.counts=TRUE)}
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+\usage{count.reads(reads_fn, I, sb=NULL, binary=FALSE, sum.counts=FALSE)}
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\arguments{
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\item{reads_fn}{filename of aligned reads in BAM format}
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\item{I}{a GRanges object giving valid genomic intervals}
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