perform_mapping: Perform GWA analysis

In AndersenLab/cegwas2: C. elegans genome-wide association

Description

perform_mapping runs association mapping on a phenotype

Usage

perform_mapping(phenotype = NULL, genotype = cegwas2::snps,
  kinship = cegwas2::kinship, P3D = FALSE, n.PC = 0,
  min.MAF = 0.05, map_by_chrom = FALSE,
  mapping_cores = parallel::detectCores(), FDR_threshold = 0.05)

Arguments

phenotype	a data frame with columns: strain and phenotype [Default: "wormbase_gene"]
genotype	a genotype matrix in the format CHROM, POS, REF, ALT, strain1, ... , strainN [Default: cegwas2::snps]
kinship	a N x N relatedness matrix in the format of [Default: cegwas2::kinship]
P3D	TRUE/FALSE - TRUE refers to the EMMAx algorithm FALSE refers to EMMA algorithm
n.PC	Integer describing the number of principal components of the genotype matrix to use as fixed effects, [Default:0]
min.MAF	a value ranging from 0 - 1 that determines the minimum minor allele frequencey a marker must have to be used in association mapping [Default: 0.05]
map_by_chrom	TRUE/FALSE - BLUP residual mappings from [Bloom, J. S. et al. 2015] [Default: FALSE]
mapping_cores	Integer, number of cores to assign to mapping
FDR_threshold	threshold for calculated FDR and Bonferroni, [Default:0.05]

Value

a dataframe with the following columns

• CHROM - Chromosome name

• POS - Physical position of marker

• marker - Marker name

• trait - Trait name of input phenotype

• BF - Bonferroni-corrected p-value threshold

• log10p - [-log10] transformation of the p-value for the indicated marker

• pval - p-value for indicated marker

• Zscore - standard score for all p-values

• qvalue - p-values adjusted by FDR

AndersenLab/cegwas2 documentation built on Aug. 26, 2020, 4:43 p.m.