mirna2mrna: A function to map miRNA to mRNA.

In jmacdon/affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips

A function to map miRNA to mRNA.

Description

This function is intended use when there are miRNA and mRNA data for the same subjects, and the goal is to detect mRNAs that appear to be targeted by the miRNA.

Usage

mirna2mrna(
  miRNAids,
  miRNAannot,
  mRNAids,
  orgPkg,
  chipPkg,
  sanger = TRUE,
  miRNAcol = NULL,
  mRNAcol = NULL,
  transType = "ensembl"
)

Arguments

miRNAids	A character vector of miRNA IDs. Currently only supports Affymetrix platform.
miRNAannot	Character. The filename (including path if not in working directory) for the file containing miRNA to mRNA mappings.
mRNAids	A character vector of mRNA IDs. Currently only supports Affymetrix platform.
orgPkg	Character. The Bioconductor organism package (e.g., org.Hs.eg.db) to be used for mapping.
chipPkg	Character. The Bioconductor chip-specific package (e.g., hgu133plus2.db) to be used for mapping.
sanger	Boolean. Is the miRNAannot file a Sanger miRBase targets file? These can be downloaded from http://www.ebi.ac.uk/enright-srv/microcosm/cgi-bin/targets/v5/download.pl
miRNAcol	Numeric. If using a Sanger miRBase targets file, leave NULL. Otherwise, use this to indicate which column of the miRNAannot file contains miRNA IDs.
mRNAcol	Numeric. If using Sanger miRBase targets file, leave NULL. Otherwise, use this to indicate which column of the miRNAannot file contains mRNA IDs.
transType	Character. Designates the type of transcript ID for mRNA supplied by the miRNAannot file. If using the Sanger miRBase files, this is ensembl. Other choices include refseq and accnum.

Details

This function is intended to take a vector of miRNA IDs that are significantly differentially expressed in a given experiment and then map those IDs to putative mRNA transcripts that the miRNAs are supposed to target. The mRNA transcript IDs are then mapped to chip-specific probeset IDs, which are then subsetted to only include those probesets that were also significantly differentially expressed.

The output from this function is intended as input for makeHmap.

Value

A list with names that correspond to each significant miRNA, and the mRNA probeset IDs that are targeted by that miRNA.

Author(s)

James W. MacDonald

See Also

makeHmap

jmacdon/affycoretools documentation built on Nov. 2, 2024, 1:29 a.m.