Detect markers with QTL effects

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Description

Performs detection of QTL effects on list of markers on a number of traits. Optional false discovery rate control can also be performed.

Usage

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detect.qtl(marker_data, trait_data, alleles, fdrc.method = "none", threshold = 0.05)

Arguments

marker_data

m x n matrix/array containing marker score data; m is the number of markers, n is the number of samples

trait_data

t x n matrix/array containing trait value data; t is the number of traits, n is the number of samples

alleles

vector containing the marker scores representing the alleles; currently supports diploids only; third entry assumed to be score for heterozygous marker

fdrc.method

string value representing method to be used for false discovery rate control; uses the p.adjust method in the R default library; default value is "none"

threshold

p-value threshold to be used for determining significant QTL effect; default value is 0.05

Value

qtl.list

list containing markers with detected significant QTL effect; has length equal to the number of traits

Author(s)

Jan Michael Yap

See Also

p.adjust

Examples

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data(sample.markers)
data(sample.traits)
alleles <- c(1,2,3)
qlist <- detect.qtl(sample.markers, sample.traits, alleles, fdrc.method="bonferroni")