plot.manhattan.LD: Plot LD pattern and MAF in a Manhattan plot

Description Usage Arguments Value Author(s) See Also Examples

Description

Function for plotting local LD pattern (relative to a pre-selected marker) on a Manhattan plot resulting from genome-wide association study (GWAS). Each marker on the plot is colored according to its LD with the reference marker. Color codes are not continuous, but LD is discretized into LD intervals. This is useful for examining signals found in a GWAS study. In addition, minor allele frequency will be plotted in the lower panel.

Usage

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  plot.manhattan.LD(data, gwas.result, chr, region,
    index.snp, p.value = 0.05, bonferroni = T,
    mafThreshold = 0.05)

Arguments

data

a gwaa.data class object as used by gwaa.data-class

gwas.result

a scan.gwaa class object as used by scan.gwaa-class

chr

chromosome nubmer (name) to be displayed

region

a vector of two coordinates to display

index.snp

index of the reference SNP

p.value

p-value threshold to visualize using red dashed line

bonferroni

logical indicating whether Bonferroni-correction shall be used for the displayed p-value threshold

mafThreshold

threshold value for minor allele frequency (MAF) – displayed as a red line on the lower panel

Value

NULL

Author(s)

Marcin Kierczak <Marcin.Kierczak@slu.se>

See Also

gwaa.data-class, scan.gwaa-class

Examples

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## Not run: 
plot.manhattan.LD()

## End(Not run)

cgmisc documentation built on May 2, 2019, 5:50 p.m.