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Rsamtools usage with URL

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

r bam alignment rsamtools
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updated by zx8754 zx8754 • written by Friederike Friederike

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

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written by zx8754 zx8754

do you know about alternative solutions?

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written by Friederike Friederike

Maybe download first, then read?

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written by zx8754 zx8754

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

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written by Friederike Friederike

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