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

In cgmisc-team/cgmisc: Various functions useful in computational genetics, e.g. in GWAS

Plot LD pattern and MAF in a Manhattan plot

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

plot.manhattan.genes(data, gwas.result, chr, region, index.snp,
  p.value = 0.05, mafThreshold = 0.05, bed.path = NULL)

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 number (name) to be displayed
region	a vector of two coordinates to display
index.snp	index marker of the reference SNP (name of the marker)
p.value	p-value threshold to visualize using red dashed line
mafThreshold	threshold value for minor allele frequency (MAF) – displayed as a red line on the lower panel
bonferroni	logical indicating whether Bonferroni-correction shall be used for the displayed p-value threshold
legend.pos	a string specifying position of the legend on the plot: "def.left", "def.right" or any other accepted by legend

Author(s)

Marcin Kierczak <[e-mail]>

See Also

gwaa.data-class, scan.gwaa-class

Examples

## Not run: 
plot.manhattan.genes(data=data.mh1.qc1, gwas.result=mm.mh1, chr=36, region=c(16e6,21e6),
                  index.snp="BICF2P12960", bonferroni=F, legend.pos="default")

## End(Not run)

cgmisc-team/cgmisc documentation built on Jan. 3, 2024, 9:52 p.m.