Usage Arguments Details Author(s)
1 2 3 | GRSD.assoc(pheno, pheno.col, probs, K, addcovar, markers, snp.file,
outdir = "~/Desktop/", tx = c("Gamma", "HZE", "Unirradiated", "All"),
sanger.dir = "~/Desktop/R/QTL/WD/HS.sanger.files/")
|
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(). |
Dec. 29, 2015
Elijah F Edmondson, elijah.edmondson@gmail.com
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