DESeq1: Standard process for DESeq2 RNA-Seq differencial expression...

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

Description

DESeq1 is a customed way to use DESeq2 package for differencially expression analysis based on raw counts and design object,and create a DESeqList with dds,difSig and siggenes object.

Usage

DESeq1(counts, design, contrast.col, contrast.level = c("Control",
  "Treat"), contrast.control = "Control", count.filter = 10,
  cutoff.lFC = 1, cutoff.padj = 0.1, report = F, save.file = T,
  names = "love")

Arguments

counts	raw counts matrix
design	design object with sample rows and clinic feature cols
contrast.col	the colnames of contrast.Like "N.status"
count.filter	the rowmean filter of counts
cutoff.lFC	the cutoff of log foldchange
cutoff.padj	the cutoff of adjusted P value
report	whether to do quality control report.Default is F.
save.file	whether to save .rda object for DESeqList
names	part name of saved files

Value

DESeqList

Author(s)

Weibin Huang<[e-mail]>

See Also

DESeqDataSetFromMatrix;DESeq;

Examples

library(lucky)
## data preparation
data("rna.counts")
data("rna.design")
counts = rna.counts;rm(rna.counts)
design = rna.design;rm(rna.design)

## DESeq2 package standard pipeline
dl1 <- DESeq1(counts,
              design,
              contrast.col= "condition",
              contrast.level =  c("normal","tumor"),
              contrast.control = "normal",
              count.filter=10,
              cutoff.lFC = 2,
              cutoff.padj = 0.05,
              save.file = F,
              names = "love",
              report = T)
View(dl1)

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