Rsamtools usage with URL

Question

[Friederike]

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

[zx8754]

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

[Friederike]

do you know about alternative solutions?

[zx8754]

Maybe download first, then read?

[Friederike]

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

[zx8754]

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