Question: an error in TvTi: package GenVisR
gravatar for Bogdan
11 months ago by
Palo Alto, CA, USA
Bogdan480 wrote:

Dear all,

please if you can please advise me on the following : I am using the package GenVisR in order to plot TvTi data on a MAF file that is formatted as below :

> head(maf_protein)
   Hugo_Symbol Entrez_Gene_Id   Center NCBI_Build Chromosome Start_Position
1:    ANKRD36B             NA STANFORD       hg38       chr2       97558820
2:       POTEE             NA STANFORD       hg38       chr2      131238210
3:    ADAMTSL1             NA STANFORD       hg38       chr9       18770622
4:     FOXD4L6             NA STANFORD       hg38       chr9       41127137
5:      BRINP1             NA STANFORD       hg38       chr9      119167786
6:        PKN3             NA STANFORD       hg38       chr9      128705466
   End_Position Strand Variant_Classification Variant_Type Reference_Allele
1:     97558820      +      Missense_Mutation          SNP                C
2:    131238210      +      Missense_Mutation          SNP                T
3:     18770622      +                 Silent          SNP                G
4:     41127137      +      Missense_Mutation          SNP                G
5:    119167786      +                 Silent          SNP                G
6:    128705466      +      Missense_Mutation          SNP                G
   Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS Tumor_Sample_Barcode
1:                 C                 T       NA                   AA
2:                 T                 C       NA                   AA
3:                 G                 A       NA                   CC
4:                 G                 C       NA                   CC
5:                 G                 T       NA                   CC
6:                 G                 A       NA                   CC
   Mutation_Status AAChange Transcript_Id TxChange GeneDetail.refGene
1:         Somatic  p.E316K     NM_025190  c.G946A                  .
2:         Somatic  p.L405P  NM_001083538 c.T1214C                  .
3:         Somatic  p.G746G  NM_001040272 c.G2238A                  .
4:         Somatic  p.P416R  NM_001085476 c.C1247G                  .
5:         Somatic  p.L528L     NM_014618 c.C1584A                  .
6:         Somatic   p.R63H     NM_013355  c.G188A                  .

However, I am getting the following error (below). Any suggestions please on how I can fix it ? Thanks !!!

>TvTi(maf_protein, lab_txtAngle=75, fileType="MAF")
Found appropriate columns
Removed 249 indels present in data
annotating transitions and transversions
  |======================================================================| 100%
Error in data.table::data.table(...) :
  Item 1 has no length. Provide at least one item (such as NA, NA_integer_ etc) to be repeated to match the 2292 rows in the longest column. Or, all columns can be 0 length, for insert()ing rows into.
ADD COMMENTlink modified 11 months ago by zlskidmore10 • written 11 months ago by Bogdan480
gravatar for zlskidmore
11 months ago by
zlskidmore10 wrote:

It looks like the maf_protein variable is storing a data.table object and not a data.frame object. I'm not sure why this would cause an issue, I suspect the issue may be the plyr package which GenVisR uses is unable to handle objects of class data.table. I'm investigating further now. Does coercing to a data.frame solve the issue?


TvTi(, lab_txtAngle=75, fileType="MAF")


ADD COMMENTlink written 11 months ago by zlskidmore10

Thank you very much, the issue is solved ;)

ADD REPLYlink written 11 months ago by Bogdan480
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