README.md

In Jiahao-Kuang/seqanalyseR: a package to analyse seq data

seqanalyseR

示例文档

在data中添加了示例文件，count.txt为生数据，group.csv为分组文件 data<-read.table(file = "count.txt",header = T) group<-read.csv(file = "group.csv",header = T) group2<-read.csv(file = "group.csv",header = T,row.names = 1)

下游分析全过程函数

DOWNSTREAManalysis(DATA = data,GROUP = group,SPECIES = "RAT",GENE_TYPE = "ENSEMBL")

转换ID

aa<-IDchange( geneIDtoCHANGE = row.names(data), CHANGEfromTYPE = "ENSEMBL", CHANGEtoTYPE = "ENTREZID", SPECIES = "RAT", omitNA = TRUE, MERGEtoDATA = data, drop = TRUE )

差异分析

bb<-differenceANALYSIS1(rawdata = data,group = group,omitNA = T)

GO富集（KEGG同理）

GO<-GOenrich(aa$ENTREZID, SPECIES = "RAT")

火山图

plotVOCANOL(bb, LOG2FC = 0.05, PVALUE =0.05, TAQ = FALSE,#(可以提供感兴趣基因的列表) TITAL = "火山图")

热图

plotHEATMAP1(bb, group2) #分组文件2（行名为样品名，第一列为分组）)

点图

f<- plotDOT1(GO) f<- plotDOT2(GO)

条状图

g<- plotBAR(KEGG)

Jiahao-Kuang/seqanalyseR documentation built on May 7, 2023, 11:27 a.m.