R: Method to add a slot of SNPs to 'MultiDataSet'.

add_snps {MultiDataSet}

R Documentation

Method to add a slot of SNPs to `MultiDataSet`.

Description

This method adds or overwrites the slot "snps" of an MultiDataSet with the content of the given SnpSet. The fData of the SnpSet must contain the columns chromosome and position.

Usage

add_snps(object, snpSet, ...)

Arguments

`object`	`MultiDataSet` that will be filled.
`snpSet`	`SnpSet` to be used to fill the slot.
`...`	Arguments to be passed to `add_eset`.

Value

A new MultiDataSet with the slot "snps" filled.

Examples

multi <- createMultiDataSet()
geno <- matrix(c(3,1,2,1), ncol = 2)
colnames(geno) <- c("VAL0156", "VAL0372")
rownames(geno) <- c("rs3115860", "SNP1-1628854")
map <- AnnotatedDataFrame(data.frame(chromosome = c("chr1", "chr2"), position = c(12414, 1234321),
     stringsAsFactors = FALSE))
rownames(map) <- rownames(geno)
snpSet <- new("SnpSet", call = geno, featureData = map)
pheno <- data.frame(id = c("VAL0156", "VAL0372"))
rownames(pheno) <- c("VAL0156", "VAL0372")
pData(snpSet) <- pheno
multi <- add_snps(multi, snpSet)