Run GCDH over a region

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Description

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

Usage

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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

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