An R error by using xhmmScripts in XHMM

Question

[Shingo]

Recently, I used XHMM to call CNV based on WES data. All the parameters were set to as the same as the XHMM workflow showed in the documentation xhmm_tutorial, and also the same as the filename. But I got an R error as follow when I drew CNV plots. Similarity, I even used the demo data set RUN from the documentation.

library(xhmmScripts)

PLOT_PATH="/Users/CJ/Desktop/RUN/"
OB_PREFICES="/Users/CJ/Desktop/RUN/DATA"
OB_TARGETS_TO_GENES="/Users/CJ/Desktop/RUN/annotated_targets.refseq.loci"
SAMPLE_FEATURES=NULL

XHMM_plots(PLOT_PATH, JOB_PREFICES, JOB_TARGETS_TO_GENES, SAMPLE_FEATURES)

Loading data from '/Users/CJ/Desktop/RUN/DATA' XHMM run...
Read 300 records
Read 300 records
Reading 30 x 300 named matrix
awk: calling undefined function gensub
 input record number 1, file 
 source line number 1
awk: calling undefined function gensub
 input record number 1, file 
 source line number 1
Error in strsplit(targets, ":", fixed = TRUE) : non-string argument

How do I draw the plots with the XHMM results? By the way, I used the hg19 for the reference genome. The chromosome ID begins with "chr". Thanks!

[zx8754]

Looks like the package is using certain version of awk with a gensub function, inside one their R functions, see: readNamedMatrix.R#L35

And your version of awk doesn't have gensub. Better to contact the developers.

[Bastien Hervé]

I never used this tool but are you on Unix, Windows or MacOS ? Because no pathway start with /Users/ in windows nor linux

[Shingo]

Thanks for your reply. I ran the XHMM on linux and draw the plot with the results on local Rstudio.

[Bastien Hervé]

Try to install gawk