ExomeDepth failure to run

Question

[German.M.Demidov]

Dear all,

I use a tool called ExomeDepth. 2 months ago I was able to run it and it worked well. Today I decided to analyse different samples and try to count reads:

library(ExomeDepth)
data(exons.hg19)
bams <- c(long vector of bams)
my.counts <- getBamCounts(bed.frame = exons.hg19, bam.files = bams, include.chr = F, referenceFasta = "/path/to/fasta/hg19.fa")

It worked before and it is exactly what is written in the manual: https://cran.r-project.org/web/packages/ExomeDepth/vignettes/ExomeDepth-vignette.pdf . I have R-3.6.1 and ExomeDepth 1.12 (freshly installed).

The error:

Error: RangedData objects are deprecated and the rownames setter for
  RangedData objects is now defunct. Please migrate your code to use
  GRanges or GRangesList objects instead. See IMPORTANT NOTE in
  ?RangedData

(obviously the important note says that it is deprecated)

Is there a way to fix it manually or I should wait for the update of the package?

(This is not a crucial thing, I run this tool for benchmarking, so if I won't be able to run it I'll just write it like it is, but if smb has thoughts how to fix it - I'd do this)

Answer 1

[Garan]

You could try installing from vplagnol github repository (using DevTools) to see if the dependency has been updated (GRanges)

https://github.com/vplagnol/ExomeDepth

install.packages("devtools")

library(devtools)
install_github("vplagnol/ExomeDepth")

If it hasn't then you could try raising an issue on the ExomeDepth repository.

[German.M.Demidov]

Was a good idea - did not work...

Downloading GitHub repo vplagnol/ExomeDepth@master
These packages have more recent versions available.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: rlang  (0.4.1  -> 0.4.2 ) [CRAN]
5: digest (0.6.22 -> 0.6.23) [CRAN]
1

No errors raised during installation, but same error happens...

Will probably rise an issue (even thou in whats' new section of the vignette it says "Version 1.1.12: Updated for GRanges changes"....)

[brunobsouzaa]

I've had the same issue as you... It is now fixed, just run devtools::install_github("vplagnol/ExomeDepth").

[German.M.Demidov]

That's just great! Thanks a lot!

[German.M.Demidov]

@brunobsouzaa I've done this, but now another error appears "Error in GenomicRanges::seqnames(target) : object target not found" :/ could you send the command that you use to read bam files? My script was working with ExomeDepth half a year ago, but now - errors...

[brunobsouzaa]

Hey dude, sorry for late reply. I'm loading the bam files using the exact same command that you've used.

my.counts <- getBamCounts(bed.frame = segments, bam.files = files, include.chr = FALSE, referenceFasta = '/path/to/fasta/hg19.fa')

Can you share your script? I can take a look!

[German.M.Demidov]

Hey, no worries, was saved by some guy from biostars, and by the author :) worked well! Thanks!

[ari]

Hello,

I am now using a software called DECoN to visualize CNVs. At some point, the same error that you posted above appears: "Error in GenomicRanges::seqnames(target) : error in evaluating the argument 'x' in selecting a method for function 'seqnames': Error: object target not found" Our BAM file does have the "chr" prefix, the target .bed file does not and neither does the reference genome file. Do you know what this error means and how to solve it? I know that is something related with the "chr" naming, but we don't know how to solve it.

Thanks!