Hi All,
I have a .maf file and the format of the file are described below, I am planning to get Gene signatures for these by using deconstruct sigs, My question is While Converting to deconstructSigs input i am using sample.id = "Sample", chr = "chr", pos = "pos", ref = "ref", alt = "alt". But in m y .maf file i am not able to find the particular column i have the following header in my .maf file. I am not able to identify the suitable column in this, Kindly help me out.
Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID
sigs.input <- mut.to.sigs.input(mut.ref = sample.mut.ref, sample.id = "Sample", chr = "chr", pos = "pos", ref = "ref", alt = "alt")
Thanks in Advance, Dave,
