Error running the getBamCounts for using ExomeDepth

Question

[martapatriciaribeiroferreira]

Hi, Someone can help me with this, when I run this function I get an error that I can't understand.

my.counts <- getBamCounts(bed.frame = exons.hg19,
+ bam.files = my.bam,
+ include.chr = TRUE)

Parse 1 BAM files

$V1

[1] 2005-742_S33.bam

Levels: 2005-742_S33.bam

Now parsing 1

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

What can I do?

Thanks!

Answer 1

[tijm2000]

Hey Marta,

Didt you ever find out what the issue was? I get the same error: 'Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘scanBamHeader’ for signature ‘"list" '

when I am trying to run scanBamHeader on my BAM file

Kind regards, Tijmen

[Matthias Zepper]

Can you please show the output of class(...) when run on whatever variable name you provide to bam.files ? And if it is "list", run a lapply(...,class) on that?