miRmine {miRmine} | R Documentation

## miRmine dataset

### Description

miRmine dataset, from Panwar et al (2017) miRmine: A Database of Human miRNA Expression

### Usage

    data("miRmine")

### Format

`miRmine` A 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

### Examples

    ## Not run:
    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
        )

    ## End(Not run)

[Package miRmine version 1.12.0 Index]