#' @importFrom DESeq2 fpkm
#' @importFrom dplyr filter_all
#' @importFrom reshape2 melt
#' @importFrom ggplot2 ggplot
globalVariables(".")
NULL
#' Calculates FPKM from DESeq2 object
#' @param DESeq2_object created using feat2deseq2 function
#' @param feat_count A tsv file from featurecount
#' @param outdir A folder to write all the files
#'
#'
#' @return creates CSV fpkm table base off DEDeq2 object
#'
#' @export
#'
#'
DESeq2FPKM <- function(DESeq2_object, feat_count, outdir){
base::ifelse(!base::dir.exists(outdir), base::dir.create(outdir), print("already exist"))
fpkm_results <- DESeq2::fpkm(DESeq2_object, robust=TRUE)
out_fpkm <- base::file.path(outdir,
base::paste(base::strsplit(base::basename(feat_count),
".tsv")[[1]],
"_FPKM.csv", sep=""))
utils::write.csv(fpkm_results, file = out_fpkm, row.names = TRUE)
return(fpkm_results)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.