R/miRmine.R

In miRmine: Data package with miRNA-seq datasets from miRmine database as RangedSummarizedExperiment

###############################################################################
### Praparation of miRmine dataset
###############################################################################



#' @title miRmine dataset
#'
#' @description miRmine dataset,
#' from Panwar et al (2017) miRmine: A Database of Human miRNA Expression
#'
#' @format \code{miRmine} A \link{RangedSummarizedExperiment} object.
#'
#' For all the details on how this dataset was produced, see examples.
#'
#' @source Panwar et al (2017) miRmine: A Database of Human miRNA Expression
#'
#' @usage
#'
#' data("miRmine")
#'
#' @examples
#' \dontrun{
#' library(GenomicRanges)
#' library(rtracklayer)
#' library(SummarizedExperiment)
#' library(Biostrings)
#'
#' ext.data <- system.file("extdata", package = "miRmine")
#' hsa.gff3.file = file.path(ext.data, "hsa.gff3")
#' mature.fa.file = file.path(ext.data, "mature.fa")
#' miRmine.info.file = file.path(ext.data, "miRmine-info.txt")
#' miRmine.tissues.file = file.path(ext.data, "miRmine-tissues.csv")
#' miRmine.cell.lines.file = file.path(ext.data, "miRmine-cell-lines.csv")
#'
#' gffRangedData.all <- import.gff3(hsa.gff3.file, genome="GRCh38")
#' gffRangedData.all$source = "miRBase v21"
#' gffRangedData.all$UniqueName = gffRangedData.all$Name
#' for (id in seq_along(as.character(gffRangedData.all$ID))){
#'     name = gffRangedData.all[id, ]$Name
#'     derives_from = gffRangedData.all[id, ]$Derives_from
#'     if (!is.na(derives_from)){
#'         precursor =
#'             gffRangedData.all[gffRangedData.all$ID == derives_from, ]$Name
#'         gffRangedData.all[id, ]$UniqueName = paste(name, precursor, sep=".")
#'     }
#' }
#' gff = gffRangedData.all[gffRangedData.all$type == "miRNA"]
#' gff = sort(gff, by=~UniqueName)
#'
#' tiss = read.csv(miRmine.tissues.file)
#' tiss$UniqueName =
#'     paste(tiss$Mature.miRNA.ID, tiss$Precursor.miRNA.ID, sep=".")
#' tiss = tiss[base::order(tiss$UniqueName), ]
#'
#' diff.names = setdiff(tiss$UniqueName, gff$UniqueName) # 7 rows differ
#'
#' cellines = read.csv(miRmine.cell.lines.file)
#' cellines$UniqueName =
#'     paste(cellines$Mature.miRNA.ID, cellines$Precursor.miRNA.ID, sep=".")
#' cellines = cellines[base::order(cellines$UniqueName), ]
#'
#' setdiff(cellines$UniqueName, gff$UniqueName) # same 7 rows differ
#'
#' tissue.mirnas.freq = base::sort(table(tiss$UniqueName))
#' gff.mirnas.freq = base::sort(table(gff$UniqueName))
#' setdiff(tissue.mirnas.freq, gff.mirnas.freq) # additional 2 rows duplicated
#' tissue.mirnas.freq[tissue.mirnas.freq > 1] # shows which rows are different
#'
#' base::rownames(
#'     tiss[(tiss$UniqueName %in%
#'         c('hsa-miR-3142.hsa-mir-3142','hsa-miR-4487.hsa-mir-4487')),])
#'
#' tiss = tiss[-c(624, 1213),]
#' tiss = tiss[!(tiss$UniqueName %in% diff.names), ]
#' cellines = cellines[-c(624, 1213),]
#' cellines = cellines[!(cellines$UniqueName %in% diff.names), ]
#'
#' mirnas.unique.names = tiss$UniqueName
#' tiss.counts =
#'     tiss[, -which(names(tiss) %in%
#'         c("UniqueName", "Mature.miRNA.ID", "Precursor.miRNA.ID"))]
#' cellines.counts =
#'     cellines[, -which(names(cellines) %in%
#'         c("UniqueName", "Mature.miRNA.ID", "Precursor.miRNA.ID"))]
#' expression = as.matrix(cbind(tiss.counts, cellines.counts))
#' rownames(expression) = mirnas.unique.names
#'
#' # add mirna sequences
#' library(Rsamtools)
#' fasta = FaFile(mature.fa.file)
#' mirna.string.set = scanFa(fasta)
#' newnames = strsplit(names(mirna.string.set), " ")
#' newnames = unlist(newnames)[ c(TRUE, rep(FALSE, 4)) ]
#' names(mirna.string.set) = newnames
#'
#' dna.strings = list()
#' for (id in seq_along(gff)){
#'     name = gff[id, ]$Name
#'     unique_name = gff[id, ]$UniqueName
#'     dna.strings[[unique_name]] = mirna.string.set[[name]]
#' }
#' gff$mirna_seq = dna.strings
#'
#' # construct RSE
#' meta = read.csv(miRmine.info.file, sep="\t")
#'
#' miRmine =
#'     SummarizedExperiment(
#'         assays=SimpleList(counts=expression),
#'         rowData=NULL,
#'         rowRanges=gff,
#'         colData=meta
#'     )
#' }
"miRmine"