letter: Subsetting a string

In Biostrings: Efficient manipulation of biological strings

Description

Extract a substring from a string by picking up individual letters by their position.

Usage

letter(x, i)

Arguments

x	A character vector, or an XString, XStringViews or MaskedXString object.
i	An integer vector with no NAs.

Details

Unlike with the substr or substring functions, i must contain valid positions.

Value

A character vector of length 1 when x is an XString or MaskedXString object (the masks are ignored for the latter).

A character vector of the same length as x when x is a character vector or an XStringViews object.

Note that, because i must contain valid positions, all non-NA elements in the result are guaranteed to have exactly length(i) characters.

See Also

subseq, XString-class, XStringViews-class, MaskedXString-class

Examples

x <- c("abcd", "ABC")
i <- c(3, 1, 1, 2, 1)

## With a character vector:
letter(x[1], 3:1)
letter(x, 3)
letter(x, i)
#letter(x, 4)             # Error!

## With a BString object:
letter(BString(x[1]), i)  # returns a character vector
BString(x[1])[i]          # returns a BString object

## With an XStringViews object:
x2 <- as(BStringSet(x), "Views")
letter(x2, i)

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, cbind, colMeans, colSums, 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, 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

[1] "cba"
[1] "c" "C"
[1] "caaba" "CAABA"
[1] "caaba"
  5-letter "BString" instance
seq: caaba
[1] "caaba" "CAABA"

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