geneInfoHT: geneInfoHT for normalization of HTseq data

In BioinformaticsFMRP/TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

geneInfoHT for normalization of HTseq data

Description

Code to generate the data “'R, eval = F library(EDASeq) library(biomaRt) #get ensembl gene IDs for hg38 ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") biomart_getID <- getBM(attributes = c("ensembl_gene_id"), mart = ensembl) #get gene length and GC content for all IDs

step <- 500 geneInfoHT <- plyr::adply(seq(1,length(biomart_getID$ensembl_gene_id),step),.margins = 1,.fun = function(x) begin <- x end <- x + step if(end > length(biomart_getID$ensembl_gene_id)) end <- length(biomart_getID$ensembl_gene_id) file <- paste0("geneInfoHT_from_",begin,"_to_",end,".rda") if(!file.exists(file)) df <- getGeneLengthAndGCContent(biomart_getID$ensembl_gene_id[begin:end] , org="hsa", mode = c("biomart")) save(df,file = file) else df <- get(load(file)) df ,.progress = "time") saveRDS(getdata, file = "getGLGC_download.RDS")a save(getdata, file = "getGLGC_download.rda") #Save output as data frame with correct header names geneInfoHT <- data.frame( geneLength = getdata[,1] , gcContent = getdata[,2] ) #Save final table save(geneInfoHT, file = "data/geneInfoHT.rda") “'

Format

A data frame with 23486 rows and 2 variables

BioinformaticsFMRP/TCGAbiolinks documentation built on April 12, 2024, 2:08 a.m.