BI_edgeR1: Differencially expression analysis via edgeR package

Description Usage Arguments Value Author(s) See Also Examples

Description

edgeR1 help do rawcounts-based differencially expression analysis via edgeR package.

Usage

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edgeRList <- edgeR1(counts,
                    design,
                    contrast.col,
                    contrast.level = c("Treat","Control"),
                    contrast.control = "Control",
                    cutoff.lFC = 1,
                    cutoff.padj = 0.1,
                    show.report = F,
                    save.file = T,
                    names = "love")

Arguments

counts

raw counts

design

design object

contrast.col

contrast colname in the design object

contrast.level

the order should be treat then control

contrast.control

the control of the contrast level

cutoff.lFC

the cut-off of log fold change

cutoff.padj

the cut-off of FDR

save.report

whether to show quality control report

save.file

whether to save edgeRList

names

part name of saved file

Value

edgeRList object that containing significant genes,significant information and edgeR fit object

Author(s)

Weibin Huang<[email protected]>

See Also

edgeR::calcNormFactors edgeR::estimateDisp edgeR::glmQLFit edgeR::glmQLFTest

Examples

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## This is a simulative process and NOT RUN
counts = data.counts;rm(data.counts)
design = design.train2
contrast.col = "N.status"
contrast.level = c("Np","N0")
contrast.contol = "N0"
count.filter=10
cutoff.lFC = 1
cutoff.padj = 0.1
save.file = T
names = "love"

## Quick Start
edgeRList <- edgeR1(counts,
                    design,
                    contrast.col,
                    contrast.level,
                    contrast.control,
                    names = "love")

## Complex Setting
edgeRList <- edgeR1(counts,
                    design,
                    contrast.col,
                    contrast.level = c("Treat","Control"),
                     contrast.level = "Control",
                    cutoff.lFC = 1,
                    cutoff.padj = 0.1,
                    save.file = T,
                    names = "love")

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.