mirna2mrna | R Documentation |
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.
mirna2mrna( miRNAids, miRNAannot, mRNAids, orgPkg, chipPkg, sanger = TRUE, miRNAcol = NULL, mRNAcol = NULL, transType = "ensembl" )
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
|
mRNAcol |
Numeric. If using Sanger miRBase targets file, leave
|
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. |
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
.
A list with names that correspond to each significant miRNA, and the mRNA probeset IDs that are targeted by that miRNA.
James W. MacDonald
makeHmap
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.