Timing Chromosomal Gains

[campbellpratt]

Hi there,
All of the data I'm using has successfully run until timing chromosomal gains. Whilst running the command I receive the following error:

Command: chrom_dup_time <- chrTime_annot (vcf, cna_data = cna_data.gk, cyto=cyto)

Error in '[.data.frame'vcf.,c("Arm", "dup.lev.")) :
undefined columns selected

The columns in data and class are all appropriate. I ran through the workflow with example data and also failed at this point . I'm unsure what I'm doing wrong so any indication would again be a massively appreciated.

[DSchreyer]

Hi,
I received the same error and can not proceed without fixing this. I checked the data multiple times and everything works fine until we get to this function.