I am trying to plot mutation spectrum:

##################################################################################################

# Construct mutational motif.

somatic.motif = mutationContext(VR, ref=BSgenome.Hsapiens.1000genomes.hs37d5)

  If I plot with full data:

plotMutationSpectrum(somatic.motif, group="sampleNames")

  it works.

  But if I get a subset of the rows, and try to plot it, it does not work.

  aster = somatic.motif[(somatic.motif@sampleNames %in% patients)]

  plotMutationSpectrum(aster, group="sampleNames")

  This gives error:

Error in colSums(y) : 'x' must be an array of at least two dimensions

  Both somatic.motif and aster are VRange objects.

  I tried to go inside of plotMutationSpectrum function, but I cannot figure out what went wrong.

  I have been struggling with this all day today.

  Could you please help me in your earliest convenience?

  Thank you very much in advance.

  Best regards,

  Haiying

After extracting a subset of mutations for 3 patients, the level of sample names stays same, somehow, and probably this was problem:

> idx = which(somatic.motif@sampleNames %in% pats[1:3])
> am = somatic.motif[idx]
>
> somatic.motif@sampleNames
factor-Rle of length 140289 with 85 runs
  Lengths:             790             451 ...            2690            1058
  Values :   B100327_T3398   B101681_T3462 ...    B88391_T2523    B99179_T3884
Levels(85): B100327_T3398 B101681_T3462 ... B88391_T2523 B99179_T3884
> am@sampleNames
factor-Rle of length 1718 with 3 runs
  Lengths:           790           451           477
  Values : B100327_T3398 B101681_T3462 B102360_T3495
Levels(85): B100327_T3398 B101681_T3462 ... B88391_T2523 B99179_T3884

But I donot know how to fix this.

I added one line after extracting subset:

aster@sampleNames = as.factor(as.character(aster@sampleNames))

and it is working now.