Entering edit mode
18 months ago
zhiyuan
•
0
Hi everyone, I downloaded a copy number somatic mutation file from ICGC, but I discovered that it was not annotated (the field "gene_affected" was blank). So I want to know where can I find annotated ICGC copy number somatic mutation files, just like gene-level copy number files in UCSC Xena? Should I set the field "gene_affected" by mapping fields "chromosome", "chromosome_start", "chromosome_end" to genome annotation row by row? Fields in this file:
names(snv_dat)
'icgc_donor_id''project_code''icgc_specimen_id''icgc_sample_id''matched_icgc_sample_id''submitted_sample_id''submitted_matched_sample_id''mutation_type''copy_number''segment_mean''segment_median''chromosome''chromosome_start''chromosome_end''assembly_version''chromosome_start_range''chromosome_end_range''start_probe_id''end_probe_id''sequencing_strategy''quality_score''probability''is_annotated''verification_status''verification_platform''gene_affected''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'