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!