shiftBed: Shift bed files

In CollapsABEL: Generalized CDH (GCDH) Analysis

Description

Generates collapsed genotypes by shifting the bed file (i.e. SNP1 collapsed with SNP2, SNP2 collapsed with SNP3, etc, when n_shift == 1).

Usage

shiftBed(rbed_info, n_shift, db_setup = FALSE, collapse_matrix = NULL)

Arguments

rbed_info	RbedInfoC object
n_shift	integer.
db_setup	logical. Whether to setup SQLite database for .bim, .fam and .frq files.
collapse_matrix	matrix of integers. See details.

Details

Collapsing matrix. The collapse_matrix parameter allows collapsing of two genotypes in a arbitrary way. Each genotype is represented by either 0, 1, 2, or 3:

0

Homozygote of the minor allele.

1

NA

2

Heterozygote.

3

Homozygote of the major allele.

The collapsing function is implemented as a matrix lookup function, i.e. Collapse(S1, S2) = CollapseMatrix[S1][S2].

The default collapsing matrix is:

0	0	0	0
0	1	1	1
0	1	0	3
0	1	3	3

Value

RbedInfoC object, with the shifted bed file path in it.

Author(s)

Kaiyin Zhong, Fan Liu

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