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Last data update: 2014.03.03

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

getSeedMatrix

R Documentation

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

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.

Examples


seedMatrix.human <- getSeedMatrix()

head(seedMatrix.human)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Roleswitch)
Loading required package: pracma
Loading required package: reshape
Loading required package: plotrix
Loading required package: microRNA
Loading required package: biomaRt
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:reshape':

    expand, rename

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DBI
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Roleswitch/getSeedMatrix.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getSeedMatrix
> ### Title: Get seed-match matrix between defined mRNA and miRNA in an
> ###   organism.
> ### Aliases: getSeedMatrix
> ### Keywords: miRNA seedmatch
> 
> ### ** Examples
> 
> 
> seedMatrix.human <- getSeedMatrix()
> 
> head(seedMatrix.human)
          name
target     hsa-miR-1 hsa-miR-100 hsa-miR-100* hsa-miR-101 hsa-miR-101*
  TSPAN6           0           0            0           0            0
  TNMD             0           0            0           0            0
  DPM1             1           0            0           1            0
  SCYL3            0           0            0           0            0
  C1orf112         1           0            0           0            0
  FGR              0           0            0           0            0
          name
target     hsa-miR-103 hsa-miR-105 hsa-miR-105* hsa-miR-106a hsa-miR-106a*
  TSPAN6             0           0            0            0             0
  TNMD               0           0            0            0             0
  DPM1               0           0            0            0             0
  SCYL3              0           1            0            0             0
  C1orf112           0           0            0            0             0
  FGR                0           0            0            0             0
          name
target     hsa-miR-106b hsa-miR-106b* hsa-miR-107 hsa-miR-10a hsa-miR-10a*
  TSPAN6              0             0           0           0            0
  TNMD                0             0           0           0            1
  DPM1                0             0           0           0            0
  SCYL3               0             0           0           0            0
  C1orf112            0             0           0           0            0
  FGR                 0             0           0           0            0
          name
target     hsa-miR-10b hsa-miR-10b* hsa-miR-122 hsa-miR-122* hsa-miR-124
  TSPAN6             0            0           0            0           0
  TNMD               0            0           0            0           0
  DPM1               0            0           0            0           0
  SCYL3              0            0           0            0           0
  C1orf112           0            0           0            0           0
  FGR                0            0           0            0           0
          name
target     hsa-miR-124* hsa-miR-125a-3p hsa-miR-125a-5p hsa-miR-125b
  TSPAN6              0               0               0            0
  TNMD                0               1               0            0
  DPM1                0               0               0            0
  SCYL3               0               0               0            0
  C1orf112            0               0               0            0
  FGR                 0               0               0            0
          name
target     hsa-miR-125b-1* hsa-miR-125b-2* hsa-miR-126 hsa-miR-126*
  TSPAN6                 0               0           0            0
  TNMD                   0               0           0            0
  DPM1                   0               0           0            0
  SCYL3                  0               0           0            0
  C1orf112               0               0           0            0
  FGR                    0               0           0            0
          name
target     hsa-miR-127-3p hsa-miR-127-5p hsa-miR-128a hsa-miR-129*
  TSPAN6                0              0            0            0
  TNMD                  0              0            0            0
  DPM1                  0              0            0            0
  SCYL3                 0              0            0            0
  C1orf112              0              0            0            0
  FGR                   0              0            0            0
          name
target     hsa-miR-129-3p hsa-miR-129-5p hsa-miR-130a hsa-miR-130a*
  TSPAN6                0              0            0             0
  TNMD                  0              0            0             0
  DPM1                  0              0            0             0
  SCYL3                 0              0            0             0
  C1orf112              0              0            0             0
  FGR                   0              0            0             0
          name
target     hsa-miR-130b hsa-miR-130b* hsa-miR-132 hsa-miR-132* hsa-miR-133a
  TSPAN6              0             0           0            0            0
  TNMD                0             0           0            0            0
  DPM1                0             0           0            0            0
  SCYL3               0             0           1            0            0
  C1orf112            0             0           0            0            0
  FGR                 0             0           0            0            0
          name
target     hsa-miR-133b hsa-miR-134 hsa-miR-135a hsa-miR-135a* hsa-miR-135b
  TSPAN6              0           0            0             0            0
  TNMD                0           0            0             0            0
  DPM1                0           0            0             0            0
  SCYL3               0           0            0             0            0
  C1orf112            0           0            0             0            0
  FGR                 0           0            0             0            0
          name
target     hsa-miR-135b* hsa-miR-136 hsa-miR-136* hsa-miR-137 hsa-miR-138
  TSPAN6               0           0            0           0           0
  TNMD                 0           0            0           0           0
  DPM1                 0           0            0           1           0
  SCYL3                0           0            0           0           0
  C1orf112             0           0            0           0           0
  FGR                  1           0            0           0           0
          name
target     hsa-miR-138-1* hsa-miR-138-2* hsa-miR-139-3p hsa-miR-139-5p
  TSPAN6                0              0              0              0
  TNMD                  0              0              0              0
  DPM1                  0              0              0              0
  SCYL3                 0              0              0              0
  C1orf112              0              0              0              0
  FGR                   0              0              0              0
          name
target     hsa-miR-140-3p hsa-miR-140-5p hsa-miR-141 hsa-miR-141*
  TSPAN6                0              0           0            0
  TNMD                  0              0           0            0
  DPM1                  0              0           0            0
  SCYL3                 0              0           0            0
  C1orf112              0              0           0            0
  FGR                   0              0           0            0
          name
target     hsa-miR-142-3p hsa-miR-142-5p hsa-miR-143 hsa-miR-143* hsa-miR-144
  TSPAN6                0              0           0            0           0
  TNMD                  0              0           0            0           0
  DPM1                  0              0           1            0           0
  SCYL3                 0              0           0            0           0
  C1orf112              0              0           0            0           0
  FGR                   0              0           0            0           0
          name
target     hsa-miR-144* hsa-miR-145 hsa-miR-145* hsa-miR-146a hsa-miR-146a*
  TSPAN6              0           0            0            0             0
  TNMD                0           0            0            1             0
  DPM1                0           0            0            0             0
  SCYL3               0           0            0            0             0
  C1orf112            0           1            0            0             0
  FGR                 0           0            0            0             0
          name
target     hsa-miR-146b-3p hsa-miR-146b-5p hsa-miR-147 hsa-miR-147b
  TSPAN6                 0               0           0            0
  TNMD                   0               1           0            0
  DPM1                   0               0           0            0
  SCYL3                  0               0           0            0
  C1orf112               0               0           0            1
  FGR                    0               0           0            0
          name
target     hsa-miR-148a hsa-miR-148a* hsa-miR-148b hsa-miR-148b* hsa-miR-149
  TSPAN6              0             0            0             0           0
  TNMD                0             0            0             0           0
  DPM1                0             0            0             0           0
  SCYL3               0             0            0             0           0
  C1orf112            0             0            0             1           0
  FGR                 0             0            0             0           0
          name
target     hsa-miR-149* hsa-miR-150 hsa-miR-150* hsa-miR-151-3p hsa-miR-151-5p
  TSPAN6              0           0            0              0              0
  TNMD                0           0            0              0              0
  DPM1                0           0            0              0              0
  SCYL3               0           0            2              0              0
  C1orf112            0           0            0              0              0
  FGR                 0           0            0              0              0
          name
target     hsa-miR-152 hsa-miR-153 hsa-miR-154 hsa-miR-154* hsa-miR-155
  TSPAN6             0           0           0            0           0
  TNMD               0           0           0            0           0
  DPM1               0           0           0            0           0
  SCYL3              0           0           0            0           0
  C1orf112           0           0           0            0           0
  FGR                0           0           0            0           0
          name
target     hsa-miR-155* hsa-miR-15a hsa-miR-15a* hsa-miR-15b hsa-miR-15b*
  TSPAN6              0           0            0           0            0
  TNMD                0           0            0           0            0
  DPM1                0           0            0           0            0
  SCYL3               0           0            1           0            1
  C1orf112            0           0            0           0            0
  FGR                 0           0            0           0            0
          name
target     hsa-miR-16 hsa-miR-16-1* hsa-miR-16-2* hsa-miR-17 hsa-miR-17*
  TSPAN6            0             0             0          0           0
  TNMD              0             0             0          0           0
  DPM1              0             0             0          0           0
  SCYL3             0             0             0          0           0
  C1orf112          0             0             0          0           0
  FGR               0             0             0          0           0
          name
target     hsa-miR-181a hsa-miR-181a* hsa-miR-181a-2* hsa-miR-181b hsa-miR-181c
  TSPAN6              0             0               0            0            0
  TNMD                0             0               0            0            0
  DPM1                0             0               0            0            0
  SCYL3               0             0               0            0            0
  C1orf112            0             0               0            0            0
  FGR                 0             0               0            0            0
          name
target     hsa-miR-181c* hsa-miR-181d hsa-miR-182 hsa-miR-182* hsa-miR-183
  TSPAN6               0            0           0            0           0
  TNMD                 0            0           0            0           0
  DPM1                 0            0           0            0           0
  SCYL3                0            0           0            0           0
  C1orf112             0            0           1            0           0
  FGR                  0            0           0            1           0
          name
target     hsa-miR-183* hsa-miR-184 hsa-miR-185 hsa-miR-185* hsa-miR-186
  TSPAN6              0           0           0            0           0
  TNMD                1           0           0            0           0
  DPM1                0           0           0            0           0
  SCYL3               0           0           0            0           0
  C1orf112            0           0           0            0           0
  FGR                 0           0           0            0           0
          name
target     hsa-miR-186* hsa-miR-187 hsa-miR-187* hsa-miR-188-3p hsa-miR-188-5p
  TSPAN6              0           0            0              0              0
  TNMD                0           0            0              0              0
  DPM1                0           0            1              0              0
  SCYL3               0           0            0              0              0
  C1orf112            0           0            0              0              0
  FGR                 0           0            0              0              0
          name
target     hsa-miR-18a hsa-miR-18a* hsa-miR-18b hsa-miR-18b* hsa-miR-190
  TSPAN6             0            0           0            0           0
  TNMD               0            0           0            0           0
  DPM1               1            0           1            0           0
  SCYL3              0            0           0            0           0
  C1orf112           0            0           0            0           0
  FGR                0            0           0            0           0
          name
target     hsa-miR-190b hsa-miR-191 hsa-miR-191* hsa-miR-192 hsa-miR-192*
  TSPAN6              0           0            0           0            0
  TNMD                0           0            0           0            0
  DPM1                0           0            0           0            0
  SCYL3               0           0            0           0            0
  C1orf112            0           0            0           0            0
  FGR                 0           0            0           0            0
          name
target     hsa-miR-193a-3p hsa-miR-193a-5p hsa-miR-193b hsa-miR-193b*
  TSPAN6                 0               0            0             0
  TNMD                   0               0            0             0
  DPM1                   0               2            0             0
  SCYL3                  1               0            0             0
  C1orf112               0               0            0             0
  FGR                    0               0            0             0
          name
target     hsa-miR-194 hsa-miR-194* hsa-miR-195 hsa-miR-195* hsa-miR-196a
  TSPAN6             0            0           0            0            0
  TNMD               0            0           0            0            0
  DPM1               0            0           0            0            0
  SCYL3              0            0           0            0            0
  C1orf112           0            0           0            0            0
  FGR                0            0           0            0            0
          name
target     hsa-miR-196a* hsa-miR-196b hsa-miR-197 hsa-miR-198 hsa-miR-199a-3p
  TSPAN6               0            0           0           0               0
  TNMD                 0            0           0           0               1
  DPM1                 0            0           0           0               0
  SCYL3                0            0           0           0               0
  C1orf112             0            0           0           0               0
  FGR                  0            0           0           0               0
          name
target     hsa-miR-199a-5p hsa-miR-199b-5p hsa-miR-19a hsa-miR-19a* hsa-miR-19b
  TSPAN6                 0               0           1            0           1
  TNMD                   0               0           0            0           0
  DPM1                   0               0           0            0           0
  SCYL3                  0               0           0            0           0
  C1orf112               0               0           0            1           0
  FGR                    0               0           0            0           0
          name
target     hsa-miR-19b-1* hsa-miR-19b-2* hsa-miR-200a hsa-miR-200a*
  TSPAN6                0              0            0             0
  TNMD                  0              0            0             0
  DPM1                  0              0            0             1
  SCYL3                 0              0            0             0
  C1orf112              0              0            0             0
  FGR                   0              0            0             0
          name
target     hsa-miR-200b hsa-miR-200b* hsa-miR-200c hsa-miR-200c* hsa-miR-202
  TSPAN6              0             0            0             0           0
  TNMD                0             0            0             0           0
  DPM1                1             0            1             0           0
  SCYL3               0             0            0             0           0
  C1orf112            0             0            0             0           0
  FGR                 0             0            0             0           0
          name
target     hsa-miR-202* hsa-miR-203 hsa-miR-204 hsa-miR-205 hsa-miR-206
  TSPAN6              0           0           0           0           0
  TNMD                0           0           0           0           0
  DPM1                0           1           0           0           1
  SCYL3               0           0           0           0           0
  C1orf112            0           0           0           0           1
  FGR                 0           0           0           0           0
          name
target     hsa-miR-208 hsa-miR-208b hsa-miR-20a hsa-miR-20a* hsa-miR-20b
  TSPAN6             0            0           0            0           0
  TNMD               0            0           0            0           0
  DPM1               0            0           0            0           0
  SCYL3              0            0           0            0           0
  C1orf112           0            0           0            0           0
  FGR                0            0           0            0           0
          name
target     hsa-miR-20b* hsa-miR-21 hsa-miR-21* hsa-miR-210 hsa-miR-211
  TSPAN6              0          0           0           0           0
  TNMD                0          0           0           0           0
  DPM1                0          0           0           0           0
  SCYL3               0          0           0           0           0
  C1orf112            0          0           0           0           0
  FGR                 0          0           0           0           0
          name
target     hsa-miR-212 hsa-miR-214 hsa-miR-214* hsa-miR-215 hsa-miR-216a
  TSPAN6             0           0            0           0            0
  TNMD               0           0            0           0            0
  DPM1               0           0            0           0            0
  SCYL3              0           0            0           0            0
  C1orf112           0           0            0           0            0
  FGR                0           0            0           0            0
          name
target     hsa-miR-216b hsa-miR-217 hsa-miR-218 hsa-miR-218-1* hsa-miR-218-2*
  TSPAN6              0           1           0              0              0
  TNMD                0           0           0              0              0
  DPM1                0           0           0              0              0
  SCYL3               0           1           0              0              0
  C1orf112            0           0           0              0              0
  FGR                 0           0           0              0              0
          name
target     hsa-miR-219-1-3p hsa-miR-219-2-3p hsa-miR-219-5p hsa-miR-22
  TSPAN6                  0                0              0          0
  TNMD                    0                0              1          0
  DPM1                    0                0              0          0
  SCYL3                   1                1              0          1
  C1orf112                0                0              0          0
  FGR                     0                0              0          0
          name
target     hsa-miR-22* hsa-miR-220 hsa-miR-220b hsa-miR-220c hsa-miR-221
  TSPAN6             0           0            0            0           0
  TNMD               0           0            0            0           0
  DPM1               0           0            0            0           0
  SCYL3              0           0            0            0           0
  C1orf112           0           0            0            0           0
  FGR                0           0            0            0           0
          name
target     hsa-miR-221* hsa-miR-222 hsa-miR-222* hsa-miR-223 hsa-miR-223*
  TSPAN6              0           0            0           0            0
  TNMD                0           0            0           0            0
  DPM1                0           0            1           0            0
  SCYL3               0           0            0           0            0
  C1orf112            0           0            0           0            0
  FGR                 0           0            0           0            0
          name
target     hsa-miR-224 hsa-miR-23a hsa-miR-23a* hsa-miR-23b hsa-miR-23b*
  TSPAN6             0           0            0           0            0
  TNMD               0           0            0           0            0
  DPM1               0           0            0           0            0
  SCYL3              0           0            0           0            0
  C1orf112           0           0            0           0            0
  FGR                0           0            0           0            0
          name
target     hsa-miR-24 hsa-miR-24-1* hsa-miR-24-2* hsa-miR-25 hsa-miR-25*
  TSPAN6            0             0             1          0           0
  TNMD              0             0             0          0           0
  DPM1              0             0             0          0           0
  SCYL3             0             0             0          0           0
  C1orf112          0             0             0          0           0
  FGR               0             0             0          0           0
          name
target     hsa-miR-26a hsa-miR-26a-1* hsa-miR-26a-2* hsa-miR-26b hsa-miR-26b*
  TSPAN6             0              0              0           0            0
  TNMD               1              0              0           1            0
  DPM1               0              0              0           0            0
  SCYL3              0              0              0           0            0
  C1orf112           0              0              0           0            0
  FGR                0              0              0           0            0
          name
target     hsa-miR-27a hsa-miR-27a* hsa-miR-27b hsa-miR-27b* hsa-miR-28-3p
  TSPAN6             0            0           0            0             0
  TNMD               0            0           0            0             0
  DPM1               0            0           0            0             0
  SCYL3              0            0           0            1             1
  C1orf112           0            0           0            0             0
  FGR                0            0           0            0             0
          name
target     hsa-miR-28-5p hsa-miR-296-3p hsa-miR-296-5p hsa-miR-297 hsa-miR-298
  TSPAN6               0              0              0           0           0
  TNMD                 0              0              0           0           0
  DPM1                 0              0              0           0           0
  SCYL3                0              0              0           0           0
  C1orf112             0              0              0           0           0
  FGR                  0              0              0           0           0
          name
target     hsa-miR-299-3p hsa-miR-299-5p hsa-miR-29a hsa-miR-29a* hsa-miR-29b
  TSPAN6                0              0           0            0           0
  TNMD                  0              0           0            0           0
  DPM1                  0              1           0            0           0
  SCYL3                 1              0           0            0           0
  C1orf112              0              0           0            0           0
  FGR                   0              0           0            0           0
          name
target     hsa-miR-29b-1* hsa-miR-29b-2* hsa-miR-29c hsa-miR-29c* hsa-miR-300
  TSPAN6                0              0           0            0           0
  TNMD                  0              0           0            0           0
  DPM1                  0              0           0            0           0
  SCYL3                 0              0           0            0           0
  C1orf112              0              0           0            0           0
  FGR                   0              0           0            0           0
          name
target     hsa-miR-301a hsa-miR-301b hsa-miR-302a hsa-miR-302a* hsa-miR-302b
  TSPAN6              0            0            0             0            0
  TNMD                0            0            0             0            0
  DPM1                0            0            0             0            0
  SCYL3               0            0            0             0            0
  C1orf112            0            0            0             0            0
  FGR                 0            0            0             0            0
          name
target     hsa-miR-302b* hsa-miR-302c hsa-miR-302c* hsa-miR-302d hsa-miR-302d*
  TSPAN6               0            0             0            0             0
  TNMD                 0            0             0            0             0
  DPM1                 0            0             0            0             1
  SCYL3                0            0             0            0             0
  C1orf112             0            0             0            0             0
  FGR                  0            0             0            0             0
          name
target     hsa-miR-30a hsa-miR-30a* hsa-miR-30b hsa-miR-30b* hsa-miR-30c
  TSPAN6             0            0           0            0           0
  TNMD               0            0           0            0           0
  DPM1               0            0           0            0           0
  SCYL3              0            0           0            0           0
  C1orf112           0            0           0            0           0
  FGR                0            0           0            0           0
          name
target     hsa-miR-30c-1* hsa-miR-30c-2* hsa-miR-30d hsa-miR-30d* hsa-miR-30e
  TSPA