Error encountered while executing IdentifyFailures.R

[lakhujanivijay]

command

Rscript /home/bioinfo/RahmanTeam-DECoN-8d740c5/Linux/IdentifyFailures.R --Rdata output.prefix.RData --mincorr .98 --mincov 100 --custom FALSE

output

[1] "BEGIN IdentifyFailures.R"
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
R.oo v1.22.0 (2018-04-21) successfully loaded. See ?R.oo for help.

Attaching package: ‘R.oo’

The following objects are masked from ‘package:methods’:

    getClasses, getMethods

The following objects are masked from ‘package:base’:

    attach, detach, gc, load, save

R.utils v2.6.0 (2017-11-04) successfully loaded. See ?R.utils for help.

Attaching package: ‘R.utils’

The following object is masked from ‘package:utils’:

    timestamp

The following objects are masked from ‘package:base’:

    cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
    warnings

Error in `$<-.data.frame`(`*tmp*`, chromosome, value = character(0)) : 
  replacement has 0 rows, data has 219286
Calls: $<- -> $<-.data.frame
Execution halted

[lakhujanivijay]

I think I found out what is the issue here

Have a look at this line.

ExomeCount$chromosome <- gsub(as.character(ExomeCount$space),pattern = 'chr',replacement = '')

I don't understand what is this column ExomeCount$space and where does it exist and what it does contain?

[shizhiwen1990]

Hi,lakhujanivijay,
Have you solved this problem?

[vlakhujani]

@shizhiwen1990 No I haven't.

[Wguangzhi212]

I think I found out what is the issue here

Have a look at this line.

ExomeCount$chromosome <- gsub(as.character(ExomeCount$space),pattern = 'chr',replacement = '')

I don't understand what is this column ExomeCount$space and where does it exist and what it does contain?

I have the same issue as you when i run "Rscript IdentifyFailures.R --Rdata DECoNtest.RData --exons customNumbering.txt --mincorr .98 --mincov 100 --custom TRUE --out DECoNtest" :"The following objects are masked from ‘package:base’:

cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
warnings

Error in $<-.data.frame(*tmp*, chromosome, value = character(0)) :
replacement has 0 rows, data has 68
Calls: $<- -> $<-.data.frame"

[Wguangzhi212]

[PaolaD]

Thanks @Wguangzhi212, i had the same problem and this worked fine.
Since i also encountered a similar problem when using ExomeDepth, i just wanted to say this error is related to the ExomeDepth version you are using, since Decon use the ExomeDepth library.
In the most recent version (1.1.15) they changed the header ExomeCount$space in ExomeCount$chromosome, so IdentifyFailures.R and makeCNVcalls.R won't work...
Hope this helped to answer the "why" it doesn't work!