[Bioc-sig-seq] coverage vectors and subseq

[kirti prakash]

Hi,

I was reading the material "EMBL course on Short Read analysis with
Bioconductor: An exercise with coverage vectors" by Simon Anders.

I tried this...
aln <- readAligned("dirPath", pattern="sequence.map", type="Bowtie")
cov = coverage(aln)
cov
[[1]]
SimpleRleList of length 25
$chr1
'integer' Rle of length 247188620 with 840106 runs
 Lengths:    463     36   6823     36 550058 ...    713     36   2034     36
 Values :      0      1      0      1      0 ...      0      1      0      2

$chr10
'integer' Rle of length 135373320 with 446681 runs
 Lengths: 88078    36  3880    36 12451 ...    20    50    36 22054    36
 Values :     0     1     0     1     0 ...     1     0     1     0     1
.
.
.

>cvg <- cov$chr10
> as.vector(subseq(cvg, 123456+50, 123456-50))

Error in function (classes, fdef, mtable)  :
 unable to find an inherited method for function "subseq", for signature "list"
Error in as.vector(subseq(cvg, 123456 + 50, 123456 - 50)) :
 error in evaluating the argument 'x' in selecting a method for
function 'as.vector'

I guess * 'integer' Rle of length* should be 'numeric' Rle of length
as per the booklet ... but I don't know how to fix it.

I know I am making some stupid mistake. It would be great if anyone
can provide some help on this.

Thank you,

Best regards,

Kirti Prakash