makePythonCommands: Create commands to run helper python scripts that automate...

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

Description

Create commands to run helper python scripts that automate SNP extraction via PennCNV infer_snp_allele.pl for a cohort.

Usage

makePythonCommands(
  penn_path,
  pfb_file,
  penn_trio_list,
  triocnv_file,
  n_flanking_snp = 60,
  dataset = "TEST",
  run_dir
)

Arguments

penn_path	Full path to PennCNV installation folder
pfb_file	Full path to PFB file used in the analysis
penn_trio_list	Full path to tab-separated file, listing one trio per line in order father,mother,offspring with full paths to raw data files for each, as used in PennCNV trio
triocnv_file	Full path to annotated trio file for offspring (after inheritance map)
n_flanking_snp	Integer. A number of probes to extract in upstream and downstream flanks of CNV. Default is 60.
dataset	Dataset string used throughout the analysis. Must be consistent. Default is TEST.
run_dir	Full path to where extract the snp data. Will be incorporated into extract commands.

Value

A data table with merged sample and CNV ids as well as original tristates and counts of segments merged

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