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

In isglobal-brge/MultiDataSet: Implementation of MultiDataSet and ResultSet

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)

isglobal-brge/MultiDataSet documentation built on Oct. 9, 2021, 11:42 a.m.