search

FunGeST / Palimpsest

An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
69 stars 19 forks source link

Error in "palimpsest_plotTumorHistories" #31

Closed iS4i4S closed 4 years ago

iS4i4S commented 4 years ago

Hi again,

First thanks for the package, it works pretty well. I got I problem using the function:

palimpsest_plotTumorHistories(vcf= vcf_chrom, cna_data = maf_PCNSL_noFlags_palimpsest_v2_2, point.mut.time = point.mut.time, clonsig = signatures_exp_clonal$sig_props, subsig = signatures_exp_subclonal$sig_props, msigcol =PCNSL_signature_names)

Error in [.data.frame(cna_data, ind, c("startarm", "endarm")) : undefined columns selected

I made the following change to the code and it worked perfectly then:

dels <- unique(as.character(as.matrix(cna_data[ind, c("POS_START", "POS_END")])))

Before it was as:

dels <- unique(as.character(as.matrix(cna_data[ind, c("startarm", "endarm")])))

But... "cna_data" columns are defined as c("POS_START", "POS_END" ) ...hence causing the error

Thought it would be helpful to point out

:)

FunGeST commented 4 years ago

Thanks a lot! We will have a look and correct this. Eric