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PoisonAlien / maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
http://bioconductor.org/packages/release/bioc/html/maftools.html
MIT License
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Error:long vectors not supported yet: memory.c:3940 #1049

Open Olsennnnn opened 2 months ago

Olsennnnn commented 2 months ago

Hi, While running this laml.tnm = trinucleotideMatrix(maf = combined_maf, prefix = 'chr', add = TRUE, ref_genome = "BSgenome.Hsapiens.UCSC.hg18") , I got a mistake, like

Warning in trinucleotideMatrix(maf = combined_maf, prefix = "chr", add = TRUE,  :
  Chromosome names in MAF must match chromosome names in reference genome.
Ignorinig 4253421 single nucleotide variants from missing chromosomes chr23, chr25, chr26
-Extracting 5' and 3' adjacent bases
-Extracting +/- 20bp around mutated bases for background C>T estimation
Error in .Call2("XStringSet_letter_frequency", x, collapse, codes, baseOnly,  : 
  long vectors not supported yet: memory.c:3940

Do you have any suggestion how to solve it? Thanks

PoisonAlien commented 1 month ago

Hi,

I'm sorry for not getting back to you sooner. Chromosome names in your MAF appear to have the chr prefix already. You do not need to use the prefix argument.