gcdhRegion: Run GCDH over a region

In CollapsABEL: Generalized CDH (GCDH) Analysis

Description

A region around some SNP is extracted and GCDH analysis is conducted over that region.

Usage

gcdhRegion(pl_gwas, n_shift = NULL, snp, window = 500, out = NULL,
  gwas_col_select = collenv$.linear_header_default, collapse_matrix = NULL,
  rm_shifted_files = TRUE, dist_threshold = 5e+05)

Arguments

pl_gwas	PlGwasC object
n_shift	integer. Maximum shift number.
snp	character. SNP name
window	numeric. All variants with physical position no more than half the specified kb distance (decimal permitted) from the named variant are loaded.
out	character. Path to the regional bed file (without .bed extension).
gwas_col_select	character. See runGcdh
collapse_matrix	See runGcdh
rm_shifted_files	See runGcdh
dist_threshold	See runGcdh

Value

See runGcdh

Author(s)

Kaiyin Zhong, Fan Liu

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