subset.mpcross: Subset mpcross object

Description Usage Arguments Value Note See Also Examples

Description

Reduces an mpcross object down to a specified set of chromosomes, markers and/or lines

Usage

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## S3 method for class 'mpcross'
subset(x, groups = NULL, chr = NULL, markers = NULL,
  lines = NULL, ...)

Arguments

x

Object of class mpcross

groups

selected groups to KEEP. Default is all

chr

Selected chromosomes TO KEEP. Default is all

markers

Selected markers TO KEEP. Default is all

lines

Selected lines TO KEEP. Default is all

...

Additional arguments

Value

The original object with chromosomes/lines/markers removed which are not listed in the arguments.

Note

Chromosomes can be input either as the character names of chromosomes or the index of the chromosomes in the map. Markers can be input as character names or the index in the matrix x$finals. Lines can be input as either character values (matching the rownames of x$finals) or indices of rows in that matrix. Groups must be input as numbers corresponding to the specific groups to keep (the groups present in the object may not form a consecutive set of numbers). Note that only one of chr, groups and markers can be selected.

See Also

mpcross.object

Examples

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map <- qtl::sim.map(len=rep(100, 2), n.mar=11, include.x=FALSE, eq.spacing=TRUE)
ped <- sim.mpped(4, 1, 500, 6, 1)
sim.dat <- sim.mpcross(map=map, pedigree=ped, 
	qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), 
	nrow=2, ncol=6, byrow=TRUE), seed=1)
sim.dat
red.dat <- subset(sim.dat, chr=1, lines=1:50)
red.dat

behuang/mpMap documentation built on May 12, 2019, 10:53 a.m.