Read in multiple MGP1000 union consensus SNV & InDel mutation tables, filter based on consensus threshold or sample/gene, merge all tables, calculate VAF, and prepare for downstream use in maf2maf or maf2vcf. The bare minimum for a MAF is Chromosome, Start_Position, Reference_Allele, Tumor_Seq_Allele2, Tumor_Sample_Barcode but will also include Matched_Norm_Sample_Barcode.
Usage
get_maf_lite(
path_to_snv_dir,
path_to_indel_dir,
snv_consensus_filter = 2,
indel_consensus_filter = 2,
strict_samples = NULL,
discovery_genes = NULL,
return_type = "maf.lite"
)Arguments
- path_to_snv_dir
Path to directory of MGP1000 union consensus SNVs
- path_to_indel_dir
Path to directory of MGP1000 union consensus InDels
- snv_consensus_filter
Threshold consensus filter for SNVs
- indel_consensus_filter
Threshold consensus filter for InDels
- strict_samples
Samples that will be filtered with
*_consensus_filter``+1- discovery_genes
Gene set vector used for discovery with
*_consensus_filter``=0- return_type
Output either the converted maf-lite format table or data.table of standard format mutation table, supported: maf.lite, data.table