miR_converter: Convert miRNA annotation to the miRBase 21 version

In AllenTiTaiWang/anamiR: An integrated analysis package of miRNA and mRNA expression data

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)

AllenTiTaiWang/anamiR documentation built on May 5, 2019, 4:55 a.m.