Description Usage Arguments Details Value
View source: R/gwas_mappings.R
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.
1 2 | gwas_mappings(data, cores = parallel::detectCores(), kin_matrix = kinship,
snpset = snps, min.MAF = 0.05, mapping_snp_set = TRUE)
|
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. |
This is the detail section if you want to fill out in the future
Outputs a data frame with the following columns : marker, CHROM, POS, trait, log10p, where marker is CHROM_POS.
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