NBAMSeqDataSet: NBAMSeqDataSet constructor

In NBAMSeq: Negative Binomial Additive Model for RNA-Seq Data

Description

NBAMSeqDataSet constructor

Usage

NBAMSeqDataSet(countData, colData, design, ...)

Arguments

countData	a matrix or data frame contains gene count
colData	a DataFrame or data.frame
design	a mgcv type design. e.g. ~ s(pheno) or ~ s(pheno) + var1 + var2
...	optional arguments passed to SummarizedExperiment

Value

a NBAMSeqDataSet object

Examples

n = 100  ## n stands for number of genes
m = 20   ## m stands for sample size
countData = matrix(rnbinom(n*m, mu=100, size=1/3), ncol = m)
mode(countData) = "integer"
colnames(countData) = paste0("sample", 1:m)
rownames(countData) = paste0("gene", 1:n)
pheno = runif(m, 20, 80)
colData = data.frame(pheno = pheno)
rownames(colData) = paste0("sample", 1:m)
gsd = NBAMSeqDataSet(countData = countData,
colData = colData, design = ~s(pheno))

NBAMSeq documentation built on Nov. 8, 2020, 6:26 p.m.