peaksummary {eqtl} | R Documentation |
Print summary information about QTL contained in a peak
object.
peaksummary(peak.array,cross,exc=data.frame(inf=0,sup=0,chr=NA),graph=FALSE,...)
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. |
Return a list containing a variety of summary information about QTL distribution according to the peak
features.
No page setting has been specified in the peaksummary
function therefore if graph=TRUE
all graphs will appear one above the others within the same R graphical window. You should specified use the parameter mfrow
of the R function par()
to setup the graph page.
Hamid A. Khalili
define.peak
,read.cross
,peak.2.array
,Rsq.2.array
data(seed10); seed10 <- calc.genoprob( cross=seed10, step=2, off.end=0, error.prob=0, map.function='kosambi', stepwidth='fixed'); seed10 <- sim.geno( cross=seed10, step=2, off.end=0, error.prob=0, map.function='kosambi', stepwidth='fixed'); out.em <- scanone( seed10, pheno.col=1:50, model='normal', method='em'); 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));