can not read maf file in maftools

Question

[czz028]

I've some problems to read Maf Files (Mutation Annotation Format) in R as follows:

test = read.maf(maf = "tmp.maf", removeSilent = TRUE, useAll = TRUE) reading maf.. Using all variants. Excluding 0 silent variants.

Creating oncomatrix (this might take a while).. Sorting.. Error in oncomat.copy[, colnames(mdf)]

and the tmp.maf is: Hugo_Symbol Entrez_Gene_Id NCBI_Build Chromosome Start_Position End_Position Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele2 Protein_Change Gene dbSNP_RS Tumor_Sample_Barcode SAMD11 148398 GRCh37 1 865545 865545 Missense_Mutation SNP G A p.R28Q ENSG00000187634 rs201186828 XH0152 SAMD11 148398 GRCh37 1 865545 865545 Missense_Mutation SNP G A p.R28Q ENSG00000187634 rs201186828 XY0039 SAMD11 148398 GRCh37 1 865545 865545 Missense_Mutation SNP G A p.R28Q ENSG00000187634 rs201186828 XY0056 SAMD11 148398 GRCh37 1 865545 865545 Missense_Mutation SNP G A p.R28Q ENSG00000187634 rs201186828 XJ0007 SAMD11 148398 GRCh37 1 865545 865545 Missense_Mutation SNP G A p.R28Q ENSG00000187634 rs201186828 SS0012 SAMD11 148398 GRCh37 1 865545 865545 Missense_Mutation SNP G A p.R28Q ENSG00000187634 rs201186828 SS0177 SAMD11 148398 GRCh37 1 874762 874762 Missense_Mutation SNP C T p.R210C ENSG00000187634 rs139437968 PRB0454 NOC2L 26155 GRCh37 1 880502 880502 Missense_Mutation SNP C T p.R693Q ENSG00000188976 rs74047418 XY0033 NOC2L 26155 GRCh37 1 880922 880922 Missense_Mutation SNP C T p.D677N ENSG00000188976 rs187444884 CC_HS0268 NOC2L 26155 GRCh37 1 881784 881784 Missense_Mutation SNP C T p.V601M ENSG00000188976 rs199697037 CH0128

By the way, I use the tab Who can help? thanks!

Answer 1

[czz028]

Actually, the maf file does not work: Hugo_Symbol Entrez_Gene_Id NCBI_Build Chromosome Start_Position End_Position Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele2 Protein_Change Gene Tumor_Sample_Barcode SAMD11 148398 37 1 865545 865545 Missense_Mutation SNP G A p.R28Q ENSG00000187634 A0152 SAMD11 148398 37 1 865545 865545 Missense_Mutation SNP G A p.R28Q ENSG00000187634 A0039 SAMD11 148398 37 1 865545 865545 Missense_Mutation SNP G A p.R28Q ENSG00000187634 A0056 SAMD11 148398 37 1 865545 865545 Missense_Mutation SNP G A p.R28Q ENSG00000187634 A0007 SAMD11 148398 37 1 865545 865545 Missense_Mutation SNP G A p.R28Q ENSG00000187634 A0012 SAMD11 148398 37 1 874762 874762 Missense_Mutation SNP C T p.R210C ENSG00000187634 A0046 SAMD11 148398 37 1 874762 874762 Missense_Mutation SNP C T p.R210C ENSG00000187634 A0011 SAMD11 148398 37 1 874762 874762 Missense_Mutation SNP C T p.R210C ENSG00000187634 A0055 SAMD11 148398 37 1 874762 874762 Missense_Mutation SNP C T p.R210C ENSG00000187634 ZL0181 SAMD11 148398 37 1 874762 874762 Missense_Mutation SNP C T p.R210C ENSG00000187634 HS0195 SAMD11 148398 37 1 874762 874762 Missense_Mutation SNP C T p.R210C ENSG00000187634 P0267 SAMD11 148398 37 1 874762 874762 Missense_Mutation SNP C T p.R210C ENSG00000187634 B0454 SAMD1 26155 37 1 880502 880502 Missense_Mutation SNP C T p.R693Q ENSG00000188976 A0055