merge_mafs error

[guillaume-rs]

Hi,

I'm trying to run merge_mafs on TCGA MAF files, but I get the error below.

I was wondering if there is something wrong about column equivalence between the MAF files, or if I should use some parameter to ignore some columns?

Thank you

list_path_LAML_MAF = grep(list.files(path = "/path/gdac.broadinstitute.org_LAML.Mutation_Packager_Oncotated_Calls.Level_3.2016012800.0.0", full.names = TRUE), pattern='*MANIFEST*', invert=TRUE, value=TRUE)

test = merge_mafs(list_path_LAML_MAF, verbose = TRUE)
Merging 197 MAF files
Error in data.table::rbindlist(l = maf, fill = TRUE, idcol = "Source_MAF",  :
  Class attribute on column 168 of item 89 does not match with column 168 of item 1.

sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /path/.conda/envs/owkin/lib/libopenblasp-r0.3.15.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] maftools_2.8.0

loaded via a namespace (and not attached):
[1] compiler_4.1.0     Matrix_1.3-3       RColorBrewer_1.1-2 survival_3.2-11
[5] splines_4.1.0      grid_4.1.0         data.table_1.14.0  lattice_0.20-44

[PoisonAlien]

Hi,

It seems like it is a known data.table issue when columns differ in their attributes.

I think for now a quick fix would be to manually perform merging on selected/necessary columns. Below is a possible solution:

# only use following columns. Add other column names if you would like; for example, `HGVSp`
required.fields = c(
  'Hugo_Symbol',
  'Chromosome',
  'Start_Position',
  'End_Position',
  'Reference_Allele',
  'Tumor_Seq_Allele2',
  'Variant_Classification',
  'Variant_Type',
  'Tumor_Sample_Barcode'
)

mafs = lapply(X = list_path_LAML_MAF, function(x){
  data.table::fread(file = x, sep = "\t", select = required.fields, skip = "Hugo_Symbol")
})

mafs = data.table::rbindlist(l = mafs, use.names = TRUE, fill = TRUE, idcol = "Source_MAF")

mafs = maftools::read.maf(maf = mafs)

I haven't tested the above code but I am guessing it should work fine. Let me know if this helps.
I will look for an alternative solution meanwhile.

[guillaume-rs]

Thank you for your quick feedback.
It works fine with the filtering step on the columns !