getSeedMatrix: Get seed-match matrix between defined mRNA and miRNA in an...

In Roleswitch: Infer miRNA-mRNA interactions using paired expression data from a single sample

Description

Given N mRNA and M miRNA IDs or simply the species common names (e.g., human), obtain the N by M seed match matrix as a the number of target sites each mRNA has for each miRNA.

Usage

getSeedMatrix(mRNA, miRNA, species = "human", 
  id_type = "ensembl_transcript_id", mRNA_id_type = id_type,
  miRNA_id_type = id_type, longest3utr = TRUE, 
  biomart = "ensembl", dataset = "hsapiens_gene_ensembl",
  returnGeneInfo = FALSE, convert2genesymbol = TRUE, ...)

Arguments

mRNA	A character vector of N mRNA ids.
miRNA	A character vector of M miRNA ids
species	Common names for a species. Currently only human and mouse are supported as precompiled target site information.
id_type	A string specifying the id type used for both the mRNAs and miRNA.
mRNA_id_type	A string specifying the id type used for the mRNAs.
miRNA_id_type	A string specifying the id type used for the miRNAs.
longest3utr	For genes having multiple transcripts, whetehr to use only the transcript with the longest 3'UTR (default: TRUE).
biomart	Database for biomart, which is ued to obtain transcript information using getBM (default: ensembl).
dataset	Dataset used to query the biomart database using getBM (default: hsapiens_gene_ensembl).
returnGeneInfo	Binary indicator to return gene information besides seed matrix (default: FALSE); if TRUE, then a list containing seed matrix and gene info is return; otherwise just the seed matrix.
convert2genesymbol	Whether to convert id such as ensembl_gene_id to gene symbols as row names of the seed matrix.
...	Paramters passed to getBM.

Details

Retrieve and process target site information to generate a N by M matrix representing the number of target sites of mRNA i for miRNA k. If species is specified, then the suggested data package RoleswitchData will be loaded and the pre-compiled seed matrix is used. Currently, only human and mouse are supported with this option. Otherwise, download the sequences based on the specified mRNA and miRNA IDs and obtain the seed matches using seedRegions.

Value

seed match matrix	numeric matrix containing the number of target sites for each miRNA and mRNA pairs
gene info	a data.frame containing miRNA id type, ensembl gene id, gene symbol, start and end of 3'UTR (only returned when returnGeneInfo is TRUE)

Note

This is just a convenience function. Users are encouraged to construct the most up-to-date seed match matrix on their own from other source without using this function.

Author(s)

Yue Li

References

miRBase: tools for microRNA genomics. (2008). miRBase: tools for microRNA genomics., 36(Database issue), D154-8. doi:10.1093/nar/gkm952

R. Gentleman and S. Falcon (2013). microRNA: Data and functions for dealing with microRNAs. R package version 1.18.0.

See Also

roleswitch,getBM,seedRegions

Examples

seedMatrix.human <- getSeedMatrix()

head(seedMatrix.human)

Roleswitch documentation built on April 28, 2020, 8:29 p.m.