[BioC] bam or sam for counting

[Martin Morgan]

On 11/02/2011 01:22 PM, wang peter wrote:
> hi all:
>       usually in R, people like to use readGappedAlignments to read aligned
> bam files, it is only for
> saving momery? is there any function to read sam files?

convert the sam file to bam using Rsamtools::asBam, or use R's scan() 
and appropriate 'what=' argument; see ?scan, ?scanBam

>      for some data, especially for human, the bam file is still very large
> (more than 15 G), do you have some ways to
> deal with it partly?

use

   param = ScanBamParam(which=GRanges("chr3", IRanges(1, 10000)))

and then

   GenomicRanges::readGappedAlignments(bamFile, param=param)

or

   Rsamtools::readBamGappedAlignments(bamFile, param=param)

or

   Rsamtools::scanBam(bamFile, param=param)

'which' can be any GRanges object.

Martin

>       thx
>
> shan gao
>
> 	[[alternative HTML version deleted]]
>
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