routine1: QCDH routine 1

In kindlychung/CollapsABEL: An R package for quantitative CDH analysis

Description

This routine collects info on the working directory, performs an initial GWAS as a basis for SNP selection by p values, generates bed files with collapsed genotypes, analyzes them, and saves intermediate and final results in an environment named after the task. This routine is called by qcdhRoutine.

Usage

routine1(wDir = ".", taskName, plinkArgs, initGwas = FALSE, initGwasArgs,
  pFilter = 0.05, nMaxShift)

Arguments

wDir	Working directory. All paths within this function will be relative to this.
taskName	Name of the QCDH task.
plinkArgs	Arguments to be passed to PLINK (in QCDH analysis)
initGwas	Whether to perform an initial GWAS
initGwasArgs	Arguments to pass to PLINK for the initial GWAS
pFilter	Filter out SNPs with p value higher than this (in the initial GWAS)
nMaxShift	Maximum shift number (for genotype collapsing)

Value

hubtask An environment containing info and results from the current task.

kindlychung/CollapsABEL documentation built on May 20, 2019, 9:57 a.m.