Given an input set of seed regions and a set of sequences all locations
of the seed regions (exact matches) within the sequences are found.
Usage
matchSeeds(seeds, seqs)
Arguments
seeds
The seeds, or short sequences, to match.
seqs
The sequences to find matches in.
Details
We presume that the problem is an exact matching problem and that
all sequences are in the correct orientation for that. If, for
example, you start with seed regions from a microRNA (for seeds)
and 3'UTR sequences (for seqs), then you would want to reverse
complement one of the two sequences. And make sure all sequences
are either DNA or RNA.
Names from either seeds or seqs are propogated, as much
as is possible.
Value
A list containing one entry for each element of seeds that had
at least one match in one entry of seqs. Each element of this list
is a named vector containing the elements of seqs that the corresponding
seed has an exact match in.
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(microRNA)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/microRNA/matchSeeds.Rd_%03d_medium.png", width=480, height=480)
> ### Name: matchSeeds
> ### Title: A function to match seed regions to sequences.
> ### Aliases: matchSeeds
> ### Keywords: manip
>
> ### ** Examples
>
> library(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:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: XVector
> data(hsSeqs)
> data(s3utr)
> hSeedReg = seedRegions(hsSeqs)
> comphSeed = as.character(reverseComplement(RNAStringSet(hSeedReg)))
> comph = RNA2DNA(comphSeed)
> mx = matchSeeds(comph, s3utr)
>
>
>
>
>
> dev.off()
null device
1
>