lixiangchun / deciphermutationalsignatures Goto Github PK

Hi,
What would be the .maf file format to be used? i am not able to find library(cgat), how can i download this.
Also, it would be of great help if you can let me know the way to run "prepareInputsForDecipherMutationalSignatures(maf.file, strand.bias=FALSE)" command, since Library(CGAT) is not available to install.

My maf file consists of the following header --> is this suffice or should i convert this into some other format? if yes what tool i need to consider.

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 | Verification_Status | Mutation_Status | Sequence_Source | Validation_Method | icgc_mutation_id | icgc_donor_id | project_code | icgc_specimen_id | matched_icgc_sample_id | submitted_sample_id | submitted_matched_sample_id | mutation_type | quality_score | probability | total_read_count | mutant_allele_read_count | biological_validation_platform | consequence_type | aa_mutation | cds_mutation | transcript_affected | gene_build_version | platform | experimental_protocol | base_calling_algorithm | alignment_algorithm | variation_calling_algorithm | other_analysis_algorithm | seq_coverage | raw_data_repository | raw_data_accession | initial_data_release_date | ens_id

Thanks a lot for your kind help.
Ateeq

Hello Xiangchun:

could you able to share the R function "prepareInputsForDecipherMutationalSignatures" to preparing our data for mutation signature? Thanks.

Hello:

I am very interested to run deciphermutaitonsignature as you changed from original framework. Could you able to share the cgat package for the plot? Thanks so much.

library(cgat) ## Cancer Genome Analysis Toolkit (cgat), will be available on Github soon.