readInputs: Load and combine multiple input files

In aksenia/SeeCiTe: Assess the quality of and visualize array CNV callset for trios

Description

Load and combine multiple input files

Usage

readInputs(args)

Arguments

args

A list holding all necessary data files. eg "triocnv_file" (input formatted penn triocnv file for offspring), "probecoord_file" (file created by _runcommands script in flanks ), "snp_flank_file" (_candidateCnv.txt file in flanks), "snp_cnv_log_file" (_candidateCnvLOG.txt file in cnv locus), "cnv_qcsum_file" (*.qcsum file from PennCNV), "dataset" (dataset string used throughout the analysis), "cache_id" (full path to where to store rds cache files for computation havier steps), "merge_trace" (table in a custom format with original PennCNV trio status and merging statistics, use runExtractInheritance to create this table)

Value

A list with "data": a data table with SNP level values of LRR and BAF for each individual in a trio; if "cnv_qcsum_file" in args is supplied, a "qcsum" table with the genome-wide LRR and BAF summaries for each individual; if "merge_trace" in args is supplied, a "merge" table with original PennCNV trio states and merging segment counts

aksenia/SeeCiTe documentation built on Jan. 19, 2021, 12:35 a.m.