testBatchEffect: test and remove potencial batch effects

In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

Description

testBatchEffect help test potencial and specified fators that may bring batch effect base on DESeq2 pipeline

Usage

testBatchEffect(SigObject, design = NULL, candidate = c("gender",
  "diognosis.year"), n.sv = NULL, names = "love", report = T)

Arguments

SigObject	the result of DESeq1, edgeR1 or a expression matrix
design	design object.If SigObject is a matrix,it is needed.
candidate	the candidate variables you selectd like years or days
names	the name of saved file
report	whether to show plot reports

Author(s)

Weibin Huang<[e-mail]>

See Also

DESeq1.

Examples

## This is a simulative process and available only with CORRECT VARIABLES
coldata <- as.data.frame(colData(SigObject$dds))
colnames(coldata)
candidate=c("gender","diognosis.year","pT")
t.be <- testBatchEffect(SigObject,
                        candidate,
                        names = "test")
View(t.be)
View(t.be$Unknown$SigTest)

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