PSAR: One-step function performing differential expression analysis...

In JungsooGIM/PSARseq: Population stratification analysis for RNA-Seq data

Description

One-step function performing differential expression analysis adjusting population stratification

Usage

PSAR(Obj, grps, n.factor = 2)

Arguments

Obj	An input object: SeqExpressionSet (EDASeq), DGEList (edgeR) or raw count in "matrix" class are available
grps	A vector or data.frame indicating the variable to be tested (in case of data.frame, the first column should be the variable to be tested)
n.factor	The number of factors in non-negative factorization (default = 2)

Details

See the referenced paper.

Value

resOut

a list of including two variables: dgeset (DGEList) and fit (glmFit)

Author(s)

Jungsoo Gim

References

Jungsoo Gim and Christoph Lange, PSARseq (2017)

Examples

cnts <- matrix(rnbinom(1000, mu=10, size=1), nrow=100)
grps <- factor(rep(c("a", "b"), each=5))
res <- PSAR(cnts, grps, n.factor=1)
head(DEGs(res))

JungsooGIM/PSARseq documentation built on May 16, 2019, 10:04 a.m.