IdentifyFailures Error

[bioxu]

Thanks a lot for this great tool.

I ran command "Rscript IdentifyFailures.R --RData test.RData --mincorr .98 --mincov 100 --exons target_bed_exon.txt --out test", and error as following message,

• The library is already synchronized with the lockfile.
  [1] "BEGIN IdentifyFailures.R"
  Loading required package: R.oo
  Loading required package: R.methodsS3
  R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
  R.oo v1.25.0 (2022-06-12 02:20:02 UTC) successfully loaded. See ?R.oo for help.

Attaching package: ‘R.oo’

The following object is masked from ‘package:R.methodsS3’:

throw

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

getClasses, getMethods

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

attach, detach, load, save

R.utils v2.12.0 (2022-06-28 03:20:05 UTC) 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, isOpen, nullfile, parse, warnings

Error in cor(ReadDepths) : supply both 'x' and 'y' or a matrix-like 'x'
Execution halted

Thanks a lot.

[bioxu]

Error was in DECoN version 2.0.0

[ducerer]

Meet same error, how to solve this?

[fishcakess]

Meet same error, how to solve this?

Are you trying to run this with only 1 BAM file / BAI file? I was and I got this error.

You need multiple BAMs and BAIs to run this, it calculates a correlation across all samples at one stage.