R/CMString_data.R

In rpiskol/CMString: CMS classification using a selected set of genes that are profiled using the NanoStrin echnology

#' CIT data set
#'
#' A dataset containing gene expression data for 566 samples from patients with early stage CRC.
#' The data is available from GEO ID GSE39582
#'
#' @format An ExpressionSet with 20192 features and 566 samples
#'
#' @source \url{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39582}
"exprs.CIT"

#' MVRM data set
#'
#' A dataset containing gene expression data for 522 samples from patients with early stage CRC.
#' The data is available from GEO IDs GSE17536, GSE17537, GSE14333
#'
#' @format An ExpressionSet with 20192 features and 522 samples
#'
#' @source \url{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17536}
#' @source \url{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17537}
#' @source \url{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14333}
"exprs.MVRM"

#' CRC cell line data set
#'
#' A dataset containing gene expression data for 40 samples (4 cell lines, 2 implantation locations, 5 replicates)
#' The data is available from GEO IDs NNN
#'
#' @format An ExpressionSet with 30727 features and 522 samples
#'
#' @source \url{https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=NNN}
"exprs.crc.celllines"

#' Procured patient data set
#'
#' A dataset containing gene expression data for 312 samples (182 primary, 130 met) that were profiled using NanoString
#'
#' @format An ExpressionSet with 819 features and 312 samples
"exprs.Procured"