Question: ExomeDepth failure to run
1
gravatar for German.M.Demidov
10 weeks ago by
Tuebingen
German.M.Demidov1.4k wrote:

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)

cnv exomedepth • 222 views
ADD COMMENTlink modified 10 weeks ago by Garan610 • written 10 weeks ago by German.M.Demidov1.4k
2
gravatar for Garan
10 weeks ago by
Garan610
United Kingdom
Garan610 wrote:

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.

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by Garan610

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"....)

ADD REPLYlink written 10 weeks ago by German.M.Demidov1.4k
1

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

ADD REPLYlink written 7 weeks ago by brunobsouzaa60

That's just great! Thanks a lot!

ADD REPLYlink written 7 weeks ago by German.M.Demidov1.4k

@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...

ADD REPLYlink written 6 weeks ago by German.M.Demidov1.4k

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!

ADD REPLYlink modified 17 days ago • written 17 days ago by brunobsouzaa60

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

ADD REPLYlink written 17 days ago by German.M.Demidov1.4k
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