In Tong-Chen/YSX: For Yishengxin Training

library(DESeq2)
library("RColorBrewer")
library("gplots")
library("amap")
library("ggplot2")
library("BiocParallel")

output_prefix = "ehbio"
file = "salmon.output"
sampleFile = "sampleFile"
design="conditions"
tx2gene="genome/GRCh38.tx2gene"
type="salmon"
padj=0.05
log2FC=1

分步法

dds <- salmon2deseq(file, sampleFile, design=design, tx2gene=tx2gene)
normexpr <- deseq2normalizedExpr(dds)

normalizedExpr2DistribBoxplot(normexpr, 
                              saveplot=paste(output_prefix, "DESeq2.normalizedExprDistrib.pdf", sep="."))

clusterSampleHeatmap2(normexpr$rlog, 
                      output_cor=paste(output_prefix, "DESeq2.sampleCOrrelation.txt", sep="."), 
                      saveplot=paste(output_prefix, "DESeq2.sampleCOrrelation.pdf", sep="."))

multipleGroupDEgenes(dds, design=design, output_prefix=output_prefix, padj=padj, log2FC=log2FC)

一步法

DESeq2_ysx(file, sampleFile, design=design, type=type, tx2gene=tx2gene, 
           output_prefix=output_prefix, padj=padj, log2FC=log2FC)

Tong-Chen/YSX documentation built on Jan. 25, 2021, 2:49 a.m.