View source: R/subset.mppData.R
subset.mppData | R Documentation |
mppData
objectPull out a specified set of markers and/or genotypes from a mppData
object.
## S3 method for class 'mppData'
subset(x, mk.list = NULL, gen.list = NULL, ...)
x |
An object of class |
mk.list |
Optional |
gen.list |
Optional |
... |
Ignored. |
Return:
The mppData object but with only the specified subset of data.
Vincent Garin
### Marker subset
data(mppData)
# Random selection of markers
mk.list <- sample(mppData$map[, 1], 50)
mppData_sub <- subset(x = mppData, mk.list = mk.list)
# Selection of chromosome 1 marker
mk.list <- (mppData$map[, 2] == 1)
mppData_sub <- subset(x = mppData, mk.list = mk.list)
### Genotype subset
# Random selection of genotypes
gen.list <- sample(mppData$geno.id, 200)
mppData_sub <- subset(x = mppData, gen.list = gen.list)
# Selection of genotype from cross 2 and 5
crosses <- unique(mppData$cross.ind)
gen.list <- mppData$geno.id[mppData$cross.ind %in% crosses[c(2, 5)]]
mppData_sub <- subset(x = mppData, gen.list = gen.list)
### Marker and genotype subset
mk.list <- sample(mppData$map[, 1], 50)
gen.list <- sample(mppData$geno.id, 200)
mppData_sub <- subset(x = mppData, mk.list = mk.list,
gen.list = gen.list)
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