rmRNAseq (version 0.1.0)

edgeRFit: Analysis of the RFI RNA-seq data Using edgeR

Description

This function analyzes the RFI RNA-seq data and simulated datasets using glmQLFTest, the Quasi-likelihood F-test in edgeR package.

Usage

edgeRFit(counts, design, Effect)

Arguments

counts

a matrix of count data.

design

a design matrix.

Effect

the effect used to simulate data, either line2, or time. This effect is considered as the main factor of interest where the status of DE and EE genes was specified.

Value

a list of 4 components

fit

output of glmQLFit function.

pv

a vector of p-values of the test for significant of Effect.

qv

a vector of q-values corresponding to the pv above.

Examples

# NOT RUN {
data(dat)
data(design)
counts <- dat[1:100,]
design <- design
Effect <- "line2"
edgeRout <- rmRNAseq:::edgeRFit(counts, design, Effect)
names(edgeRout)
# }