生信 R语言 - 技术栈

生信 R语言

Yinwen(o^^o)2024-01-07 12:21

11.芯片表达矩阵下游分析

R 复制代码

rm(list = ls())#清除所有变量
options(stringsAsFactors = F)
#BiocManager::install("CLL")
suppressPackageStartupMessages(library(CLL))
data("sCLLex")
sCLLex

R 复制代码

## ExpressionSet (storageMode: lockedEnvironment)
## assayData: 12625 features, 22 samples 
##   element names: exprs 
## protocolData: none
## phenoData
##   sampleNames: CLL11.CEL CLL12.CEL ... CLL9.CEL (22 total)
##   varLabels: SampleID Disease
##   varMetadata: labelDescription
## featureData: none
## experimentData: use 'experimentData(object)'
## Annotation: hgu95av2

R 复制代码

exprSet=exprs(sCLLex)
samples=sampleNames(sCLLex)
pData=pData(sCLLex)
#没有代码，暂未做

12.RNA-seq 表达矩阵差异分析

R 复制代码

rm(list = ls())
options(stringsAsFactors = F)
library(airway)
data("airway") #加载数据
exprSet=assay(airway)
colnames(exprSet)

R 复制代码

group_list=colData(airway)[,3]
exprSet=exprSet[apply(exprSet, 1,function(x)sum(x>1)>5),]
table(group_list)

R 复制代码

group_list

R 复制代码

exprSet[1:4,1:4]

R 复制代码

boxplot(exprSet)

R 复制代码

boxplot(log(exprSet+1))
dev.off()