A generic function for extracting a set of sequences (or subsequences) from a sequence container like a BSgenome object or other.
A BSgenome object or any other supported object.
Any additional arguments needed by the specialized methods.
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).
getSeq,BSgenome-method, XString-class, XStringSet-class
1 2 3 4 5
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"
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