getConditionSNP: Internal Function

In bahlolab/XIBD: Identity-by-Descent Analysis of the Human Genome

Description

IBD Summary Table

Usage

getConditionSNP(genotypes, snp.ld, maximum.ld.r2)

Arguments

genotypes	A data frame containing genotype information for a set of SNPs. See getGenotypes for more details.
snp.ld	A data frame generated from PLINK containing information on LD between pairs of SNPs (A and B). This data frame contains exactly 7 columns of informations: Chromosome of SNP A (type "numeric" or "integer") Base-pair position of SNP A (type "numeric" or "integer") SNP A identifier (type "character") Chromosome of SNP B (type "numeric" or "integer") Base-pair position of SNP B (type "numeric" or "integer") SNP B identifier (type "character") R-sequared LD statistic between SNP A and SNP B (type "numeric") where each row contains the LD information for a single pair of SNPs. The data frame should contain the header colnames(snp.ld)=c(CHR_A, BP_A, SNP_A, CHR_B, BP_B, SNP_B, R2)
maximum.ld.r2	A numeric value denoting the maximum linkage disequilibrium R2 value allowed between pairs of SNPs.

Details

Extracts the SNP with the largest LD with the current SNP and returns this as the condition SNP

Value

A data frame containing columns

1. Chromosome (type numeric or integer)

2. SNP identifier (type character)

3. Genetic map position (type numeric or integer)

4. Base-pair position (type numeric or integer)

5. Numeric SNP identifier (type numeric or integer)

6. Numeric condition SNP identifier (type numeric or integer)

with columns headed chr, snp_id, pos_M, pos_bp, marker.id and cond.snp.id.

bahlolab/XIBD documentation built on May 11, 2019, 5:24 p.m.