R处理输入数据——学习DEseq2包

1. names()函数：

get or set the names of one object

2. 利用DEseq2计算fpkm后fpkm转tpm

data_in = read.table("pla_cat_counts.txt", head=TRUE,row.names =1)

countData = as.data.frame(data_in)

colData = read.table("design.txt", head=TRUE)

names(colData)=c("samples","condition")

dds <- DESeqDataSetFromMatrix(countData = countData,

                                  colData = colData,

                                  design = ~ condition)

rowRanges(dds) = ebg

head(rowRanges(dds))

fpkm_out = fpkm(dds)

write.table(as.data.frame(fpkm_out), file="fpkm_out.txt",sep="\t",quote = FALSE)

###fpkmtotpm

fpkm<-read.table("fpkm_out.txt", sep = "\t", head=TRUE, row.names = 1)

head(fpkm)

fpkmToTpm <- function(fpkm){

  exp(log(fpkm) - log(sum(fpkm)) + log(1e6))

}

tpms <- data.frame(apply(fpkm,2,fpkmToTpm))

head(tpms)

colSums(tpms)    

3. 在R中查看数据类型

dim查看数据维度，mode查看数据类型，class查看数据对象类型

4. 批量输出文件

for (item in 1:groupnum){ ###遍历所有比较组

  name=paste("result",item,".txt",sep="")

5. 提取data.frame中的某行某列

group1sample <- design[design$condition == g1,][1]   ##提取design中condition=g1的行

library(dplyr)

G1tpm1<-(select(tpms,group1sample[1,]))   ##提取tpms中列名等于 group1sample[1,]的列

6. 合并列，并计算平均值

group2tpm <- cbind(G2tpm1, G2tpm2)   

mean2<- rowMeans(group2tpm, na.rm=F)