miR_converter {anamiR} | R Documentation

## Convert miRNA annotation to the miRBase 21 version

### Description

This function will convert the miRNA names from the data frame, which is produced by differExp_discrete, to the miRBase 21 version of miRNA annotation. If the input contains hundreds of miRNAs, it would take a few minutes to convert all of them.

### Usage

    miR_converter(data, remove_old = TRUE, original_version,
      latest_version = 21)

### Arguments

`data` | expression data in data.frame format, with sample name in columns and miRNA name in rows.
`remove_old` | logical value, if the miRNA is deleted in miRBase 21, should it be removed from row? Default is TRUE.
`original_version` | the original version of miRNA in input matrix. This one is necessary.
`latest_version` | choose an interger under 21, and this function would convert miRNA annotation to that version. Default is 21.

### Value

expression data in data.frame format, with sample name in columns and miRNA name for miRBase version 21 in rows.

### Examples

    ## Use the internal dataset
    data("mirna", package = "anamiR", envir = environment())
    data("pheno.mirna", package = "anamiR", envir = environment())

    ## SummarizedExperiment class
    require(SummarizedExperiment)
    mirna_se <- SummarizedExperiment(
     assays = SimpleList(counts=mirna),
     colData = pheno.mirna)

    ## Finding differential miRNA from miRNA expression data with t.test
    mirna_d <- differExp_discrete(
       se = mirna_se,
       class = "ER",
       method = "t.test"
    )

    ## Convert annotation to miRBse 21
    mirna_21 <- miR_converter(data = mirna_d, original_version = 17)

[Package anamiR version 1.8.0 Index]