GRSD.poisson: Genome wide association mapping with glm(family = poisson).

Usage Arguments Details Author(s)

Usage

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GRSD.poisson(pheno, pheno.col, probs, K, addcovar, markers, snp.file,
  outdir = "~/Desktop/", tx = c("Gamma", "HZE", "Unirradiated"))

Arguments

pheno:

data.frame containing phenotypes in columns and samples in rows. Rownames must contain sample IDs.

pheno.col:

the phenotype column to map.

probs:

3D numeric array containing the haplotype probabilities for each sample. Samples in rows, founders in columns, markers in slices. Samnple IDs must be in rownames. Marker names must be in dimnames(probs)[[3]].

K:

List of kinship matrices, one per chromosome in markers.

addcovar:

data.frame of additive covariates to use in the mapping. Sample IDs must be in rownames.

markers:

data.frame containing at least 3 columns with marker names, chr, Mb postion.

snp.file:

character string containing the full path to the Sanger SNP file containing genomic positions and SNPs. This file is created using condense.sanger.snps().

Details

Dec. 29, 2015

Author(s)

Elijah F Edmondson, elijah.edmondson@gmail.com


elijahedmondson/HZE documentation built on May 16, 2019, 3 a.m.