gwas_mappings: GWAS Mappings

In AndersenLab/cegwas: A set of functions to process phenotype data, perform GWAS, and perform post-mapping data processing for C. elegans.

Description

gwas_mappings uses the rrBLUP package function GWAS to perform association mapping for C. elegans. Uses 5% MAF SNPs from RADseq dataset from Andersen et al. 2012 and a kinship matrix generated from whole-genome sequence data. Can use user developed kinship matrix as well.

Usage

gwas_mappings(data, cores = parallel::detectCores(), kin_matrix = kinship,
  snpset = snps, min.MAF = 0.05, mapping_snp_set = TRUE)

Arguments

data	two element list. element 1 : traits. element 2: trait values with strains in columns with each row corresponding to trait in element 1
cores	number of cores on computer that you want to allocate for mapping. Default value is 4
kin_matrix	is a strainXstrain matrix. default kinship matrix is described above.
min.MAF	Allele frequency at which to remove SNPs from mapping snpset (dependent on available strains).
mapping_snp_set	is a logical statement that, if TRUE, uses a pruned SNP set that was identified from simulation studies.

Details

This is the detail section if you want to fill out in the future

Value

Outputs a data frame with the following columns : marker, CHROM, POS, trait, log10p, where marker is CHROM_POS.

AndersenLab/cegwas documentation built on March 6, 2020, 1:10 a.m.