GenomicTools (version 0.2.9.7)

plot.qtlRes: Plot an qtlRes Object

Description

The function offers informative plots for an qtlRes object.

Usage

# S3 method for qtlRes
plot(x, which=NULL, sig=0.01, verbose=TRUE,
                       log=FALSE, genome=NULL, pch=1, ...)

Arguments

x

Object of class qtlRes.

which

Specifies for which phenotypes the plot should be created.

sig

Chosen significance level.

verbose

Logical, extended feedback of the function.

log

Logical, y-axis scale is log(base=10)-scaled.

genome

Data frame with Chromosome names and lengths.

pch

Plot symbol to by used.

...

Additional plotting parameters.

Details

This function plots the test results of an qtlRes object as a Manhattan plot. In case only an qtlRes object is provided, then the genome information are estimated from this object. Alternatively, a data frame with genome information can be provided. In this case genone has to be a data.frame with the two columns chr and length, indicating the Chromosome names (similar as the ones given in qtlRes) and the corresponding lengths. The information for the human genome, Ensembl build 68, is also included can be used with using the option genome="Human68".

Examples

# NOT RUN {
# }
# NOT RUN {
data("phenoData")
data("genotData")

qtlresult <- QTL(pheno=phenoData, geno=genotData, which = 3:4)

plot(qtlresult, which=2)

# }