vcf.to.sigs.input() Error arguments imply differing number of rows: 1, 0

[alpreyes]

Hello,

I am attempting to use deconstructSigs and I am encountering an error with the vcf.to.sigs.input() function, after running with the correct input format I get

Error in data.frame(sample = sample, chr = chr[alt1], pos = pos[alt1],  : 
  arguments imply differing number of rows: 1, 0

Do you have any insight as to what is causing this error? I am willing to share a subset of the example file if needed.

[raerose01]

Hi, I have not come across this error before. Could you share some of the offending file?
Thanks!

[alpreyes]

Hi, thanks for your quick response I've attached a subset of the vcf file I am trying (the first 10 lines, no header)
vcf_to_sigs_input_ex_file.txt

I also attempted to run each step of the vcf.to.sigs.input() function separately, here are some of those outputs

> gt <- VariantAnnotation::readGT("./annotate_concatd_vcfs_output/16006-1083-2P_snp_con_concat_ANN.vcf", nucleotides = TRUE)
> gt

                                    NORMAL TUMOR
chr1:629274_G/A                     "G/A"  "G/G"
chr1:629488_T/C                     "T/C"  "T/T"
chr1:630317_A/G                     "A/G"  "A/A"
chr1:630750_C/T                     "C/T"  "C/C"
chr1:634229_A/C                     "A/A"  "A/C"
chr1:801702_G/C                     "G/C"  "G/G"
chr1:929037_G/C                     "G/C"  "G/G"
chr1:1139023_G/A                    "G/A"  "G/G"
chr1:1168098_G/T                    "G/G"  "G/T"
chr1:1782335_G/A                    "G/A"  "G/G"



> chr <- sub(":.+", "", rownames(gt))
> chr

[1] "chr1" "chr1" "chr1" "chr1" "chr1" "chr1" "chr1" "chr1" "chr1"

> pos <- as.numeric(sub("_.+", "", sub(".+:", "", rownames(gt))))
> pos
   [1]    629274    629488    630317    630750    634229    801702    929037   1139023   1168098   1782335 

> ref <- sub("[/|].+", "", sub(".+_", "", rownames(gt)))
> ref
   [1] "G" "T" "A" "C" "A" "G" "G" "G" "G" "G"



> mut <- data.frame()
>   for (sample in colnames(gt)) {
+     a1 <- sub("[/|].+", "", gt[, sample])
+     alt1 <- which(ref != a1)
+     mut <- rbind(mut, data.frame(sample = sample,
+                                  chr = chr[alt1],
+                                  pos = pos[alt1],
+                                  ref = ref[alt1],
+                                  alt = a1[alt1]))
+     a2 <- sub(".+[/|]", "", gt[, sample])
+     alt2 <- which(ref != a2 & a1 != a2)
+     mut <- rbind(mut, data.frame(sample = sample,
+                                  chr = chr[alt2],
+                                  pos = pos[alt2],
+                                  ref = ref[alt2],
+                                  alt = a2[alt2]))
+   }
Error in data.frame(sample = sample, chr = chr[alt1], pos = pos[alt1],  : 
  arguments imply differing number of rows: 1, 0

It is this last step that generates the error. any help is appreciated

Thank you!

[raerose01]

Hi, just checking, but do you get the same error when you use the example file you've sent?

[alpreyes]

Yes I was, however I was able to fix the problem by making a small addition to the code

in this step alt1 <- which(ref != a1) i add a [[1]] making the command alt1 <- which(ref != a1[[1]]) and that seemed to fix the error for me