Describe the issue
how to get mutational signatures result by using maftools?
Command
Please post your commands and the output (errors or any unexpected output)
my inputfile is a maf file :
The first three lines of the file is here:
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_RSdbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1
DVL1 1855 __UNKNOWN__ hg19 1 1275804 1275804 + Missense_Mutation SNP G G A 144365982 byFrequency b4386938_wes_t b4386937_wes_b __UNKNOWN__ __UNKNOWN__ __UNKNOWN__
Unknown __UNKNOWN__ hg19 1 1900266 1900266 + IGR SNP A A T b4386938_wes_t b4386937_wes_b __UNKNOWN__ __UNKNOWN__ __UNKNOWN__
PEX10 5192 __UNKNOWN__ hg19 1 2338106 2338106 + Intron SNP C C A b4386938_wes_t b4386937_wes_b __UNKNOWN__ __UNKNOWN__ __UNKNOWN__
Extracting 5' and 3' adjacent bases..
Extracting +/- 20bp around mutated bases for background C>T estimation..
Estimating APOBEC enrichment scores..
Performing one-way Fisher's test for APOBEC enrichment..
Error in apply(X = apobec.fisher.dat, 1, function(x) { :
dim(X) must have a positive length
Session info
Run sessionInfo() and post the output below
Describe the issue how to get mutational signatures result by using maftools?
Command Please post your commands and the output (errors or any unexpected output) my inputfile is a maf file : The first three lines of the file is here:
Then I runned:
The error message is:
Session info Run
sessionInfo()
and post the output belowso, can you tell me that why I have this error messages? The first five steps are all well