peaksummary: Print summary of QTL definition

In eqtl: Tools for analyzing eQTL experiments: A complementary to Karl Broman's 'qtl' package for genome-wide analysis

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.

Note

No page settings have been specified in the peaksummary function therefore if graph=TRUE all graphs will appear one above the other within the same R graphical window. You should specified the use by the parameter mfrow of the R function par() to setup the graph page.

Author(s)

Hamid A. Khalili

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));

eqtl documentation built on May 2, 2019, 5:42 a.m.