matchSeeds: A function to match seed regions to sequences.

In microRNA: Data and functions for dealing with microRNAs

Description

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.

Author(s)

R. Gentleman

See Also

seedRegions

Examples

library(Biostrings)
data(hsSeqs)
data(s3utr)
hSeedReg = seedRegions(hsSeqs)
comphSeed = as.character(reverseComplement(RNAStringSet(hSeedReg)))
comph = RNA2DNA(comphSeed)
mx = matchSeeds(comph, s3utr)

Example output

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

microRNA documentation built on Nov. 8, 2020, 7:50 p.m.