Question: Rsamtools usage with URL
1
gravatar for Friederike
11 months ago by
Friederike3.8k
United States
Friederike3.8k wrote:

Can anyone tell me the correct syntax for loading parts of a BAM file into R using a URL?

Since something like read.table(file = url("http://my.url.com/a-table.csv")) works fine, I hoped that it would be similarly straight-forward with Rsamtools, but this: scanBam(file = url("http://my.url.com/a-bam-file.bam")) only resulted in an error message:

(Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘scanBam’ for signature ‘"url"’ ).

Any pointers?

PS: an example BAM file URL could be this: http://chagall.med.cornell.edu/RNASEQcourse/WT_1_Aligned.sortedByCoord.out.bam

alignment rsamtools bam R • 359 views
ADD COMMENTlink modified 11 months ago by zx87547.1k • written 11 months ago by Friederike3.8k

From a quick look at manuals read.table accepts a filename, stdin, or url, but scanBam only accepts filename.

ADD REPLYlink written 11 months ago by zx87547.1k

do you know about alternative solutions?

ADD REPLYlink written 11 months ago by Friederike3.8k

Maybe download first, then read?

ADD REPLYlink written 11 months ago by zx87547.1k

well, that's exactly what I want to avoid :)

ADD REPLYlink written 11 months ago by Friederike3.8k

Sorry, that's what I thought, too. Maybe submit an issue at GitHub? Or ask at https://support.bioconductor.org/

ADD REPLYlink written 11 months ago by zx87547.1k
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