runGcdh: Run GCDH analysis

In CollapsABEL: Generalized CDH (GCDH) Analysis

Description

Runs GCDH over the given PlGwasC object. The PlGwasC object is first filtered by p-values from a plink --assoc run if a p-value threshold is given. New PlGwasC objects are generated by shifting the PLINK bed file (e.g. shift1.bed, shift2.bed, ...) one by one. A GWAS is run for each of these PlGwasC objects and results are collected into big.matrix files.

Usage

runGcdh(pl_gwas, n_shift, gwas_col_select = NULL, collapse_matrix = NULL,
  rm_shifted_files = TRUE, dist_threshold = 5e+05)

Arguments

pl_gwas	PlGwasC object
n_shift	integer. Maximum shift number.
gwas_col_select	character. Columns to read from a GWAS output file. Default to collenv$.linear_header_default
collapse_matrix	matrix. 4 by 4 matrix used for generating collapsed genotypes.
rm_shifted_files	logical. Whether to remove shifted bed files after analysis is done.
dist_threshold	integer. SNPs beyond this distance will be ignored. Default to 500kb.

Value

A list with the following members: (1) the input PlGwasC object. (2) an info data frame with CHR, BP and SNP columns. (3) One big.matrix object for each of the names in gwas_col_select

Author(s)

Kaiyin Zhong, Fan Liu

CollapsABEL documentation built on May 1, 2019, 7:28 p.m.