getSeq: getSeq

In Biostrings: Efficient manipulation of biological strings

Description

A generic function for extracting a set of sequences (or subsequences) from a sequence container like a BSgenome object or other.

Usage

getSeq(x, ...)

Arguments

x	A BSgenome object or any other supported object. Do showMethods("getSeq") to get the list of all supported types for x.
...	Any additional arguments needed by the specialized methods.

Value

An XString object or an XStringSet object or a character vector containing the extracted sequence(s).

See man pages of individual methods for the details e.g. with ?`getSeq,BSgenome-method` to access the man page of the method for BSgenome objects (make sure the BSgenome package is loaded first).

See Also

getSeq,BSgenome-method, XString-class, XStringSet-class

Examples

## Note that you need to load the package(s) defining the specialized
## methods to have showMethods() display them and to be able to access
## their man pages:
library(BSgenome)
showMethods("getSeq")

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, 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, which, which.max, which.min

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
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb

Attaching package: 'BSgenome'

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

    GenomeDescription, bsgenomeName, organism, provider,
    providerVersion, releaseDate, releaseName, species

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

    organism, species

Warning messages:
1: multiple methods tables found for 'organism' 
2: multiple methods tables found for 'species' 
3: multiple methods tables found for 'seqinfo' 
4: multiple methods tables found for 'seqinfo<-' 
5: multiple methods tables found for 'seqnames' 
Function: getSeq (package Biostrings)
x="BSgenome"

Biostrings documentation built on Nov. 8, 2020, 11:12 p.m.