countDf$fpkm <- with(countDf, countToFpkm(count, effLength)) with(countDf, all.equal(tpm, fpkmToTpm(fpkm))) countDf$effCounts <- with(countDf, countToEffCounts(count, length, effLength)) 参考: 关于readsCount、RPKM/FPKM、RPM(CPM)、TPM的理解 RNA-Seq的count、RPKM/FPKM、CPM、TPM的关系...
TPM:The transcripts per million calculation is similar to FPKM, but the difference is that all transcripts are normalized for length first. Then, instead of using the total overall read count as a normalization for size, the sum of the length-normalized transcript values are used as an indicato...
trans_tpm<-apply(count,2,Counts2TPM,effLen=effLen)head(trans_tpm)[,1:2] (2)FPKM转TPM 代码语言:javascript 复制 ##3.FPKM转TPMFPKM2TPM<-function(fpkm){exp(log(fpkm)-log(sum(fpkm))+log(1e6))}##计算TPM值 trans_tpm3<-apply(fpkms,2,FPKM2TPM)head(trans_tpm3)[,1:2] 和下载的tpm...
fpkmToTpm <-function(fpkm) { exp(log(fpkm) -log(sum(fpkm)) +log(1e6)) } countToCPM <-function( counts) { N <- sum(counts) exp(log(counts) +log(1e6) -log(N) ) } expmat %>% mutate( FPKM = countToFpkm(.$count, .$est_len) ) %>%#转FPKMmutate( TPM = countToTpm(.$...
很多时候我们得到的转录组格式为Count,例如在TCGA数据库下载的数据,如果我们想使用FPKM格式或者TPM,那么就需要转换,不过TCGA数据库也提供了FPKM的格式,貌似miRNA数据只有Count格式数据,如果想使用FPKM,就需要进行格式转换。 1、计算基因的长度,可以计算基因在染色体的起始和结束之差,也可以计算每个基因的最长转录本或所有...
countToTpm <- function(counts, effLen) { rate <- log(counts) - log(effLen) denom <- log(sum(exp(rate))) exp(rate - denom + log(1e6)) } countToFpkm <- function(counts, effLen) { N <- sum(counts) exp( log(counts) + log(1e9) - log(effLen) - log(N) ) } fpkmToTp...
###读取Count表达矩阵expMatrix<-read.table("raw_count.txt",row.names=1,header=TRUE,sep="\t")#查看前三个基因的read countexpMatrix[1:3,]sample1 sample2 sample3 sample4 sample5 sample6ENSG00000000003225014501850213653213729ENSG00000000005413312ENSG000000004195128897015691144857### read count转FPKM#要保证...
接着，设置一个函数，结合apply()函数对数据进行直接转换，最终得到每个基因对应的FPKM值。3. FPKM值转为TPM值 类似地，我们也可以设置一个函数来转换FPKM值为TPM值。通过这些步骤，我们完成了count值、FPKM值和TPM值之间的转换。在单基因分析中，通常推荐使用TPM值进行后续的分析计算。
tpm=gk.countto(frame=exprs,towhat="tpm",geneid='Ensembl',species='Human') count to fpkm 代码语言:shell 复制 fpkm=gk.countto(frame=exprs,towhat="fpkm",geneid='Ensembl',species='Human') count to cpm 代码语言:shell 复制 cpm=gk.countto(frame=exprs,towhat="cpm",geneid='Ensembl',specie...