eqtl (version 1.1-7)

peaksummary: Print summary of QTL definition

Description

Print summary information about QTL contained in a peak object.

Usage

peaksummary(peak.array,cross,exc=data.frame(inf=0,sup=0,chr=NA),graph=FALSE,...)

Arguments

peak.array

An object of class peak.array. See peak.2.array and Rsq.2.array functions for details.

cross

An object of class cross. See "qtl" package manual for read.cross function details.

exc

A data frame with columns inf, sup and chr which represent a genomic region to exclude from the summary. inf, sup,chr represents the genomic location in base pair (start and stop of the sequence to exclude respectively), chr specify the chromosome. They are single numeric values.

graph

If TRUE, print summary graphs.

...

Ignored at this point.

Value

Returns a list containing a variety of summary information about QTL distribution according to the peak feature.

See Also

define.peak,read.cross,peak.2.array,Rsq.2.array

Examples

data(seed10);

out.em <- scanone( seed10, pheno.col=1:50, model='normal', method='hk');
out.peak <- define.peak(out.em,'all');
out.peak <- calc.adef(seed10,out.em,out.peak);

data(BSpgmap);
out.peak <- localize.qtl(seed10,out.peak,BSpgmap);
out.array <- peak.2.array(out.peak);

# Whole QTL summary woth graph
par(mfrow=c(2,4));
peaksummary( out.array, seed10, graph=TRUE);
par(mfrow=c(1,1));

# QTL summary with graphs excluding the QTLs localized
# on chromosome 3 between 5000 and 6000 bp.
par(mfrow=c(2,4));
peaksummary( out.array, seed10, exc=data.frame(inf=5000,sup=6000,chr=3), graph=TRUE);
par(mfrow=c(1,1));