R/get_transcripts.R

In syyang93/analyzeR: This package contains functions that Stephanie uses for her analysis of recount RNAseq data.

#' Gets the transcripts for people who remain after filtering
#' 
#' @param counts1 data frame containing the scaled counts from rse_gene (assay(rse_gene))
#' @param with_gtex data frame with GTEx IDs
#' 
#' @export
#' 
#' @return Transcripts for those individuals


get_transcripts <- function(counts1, with_gtex) {
  indiv_count <- with_gtex[[2]]
  with_gtex <- with_gtex[[1]]
  tissue_transcripts <- counts1[,colnames(counts1) %in% with_gtex$run]
  tissue_transcripts_t <- as.data.frame(t(tissue_transcripts))
  print(paste0('confirm run identities are the same:', identical(rownames(tissue_transcripts_t), with_gtex$run)))
  tissue_transcripts_t$submitted_subject_id <- with_gtex$submitted_subject_id
  rownames(tissue_transcripts_t) <- tissue_transcripts_t$submitted_subject_id
  return(tissue_transcripts_t)
}