RemoveGaps: Remove Gap Characters in Sequences

In DECIPHER: Tools for curating, analyzing, and manipulating biological sequences

Description

Removes gaps ("-" or "." characters) in a set of sequences, either deleting all gaps or only those shared by all sequences in the set.

Usage

RemoveGaps(myXStringSet,
           removeGaps = "all",
           processors = 1)

Arguments

myXStringSet	An AAStringSet, DNAStringSet, or RNAStringSet object containing sequences.
removeGaps	Determines how gaps ("-" or "." characters) are removed in the sequences. This should be (an unambiguous abbreviation of) one of "none", "all" or "common".
processors	The number of processors to use, or NULL to automatically detect and use all available processors.

Details

The removeGaps argument controls which gaps are removed in myXStringSet. Setting removeGaps to "all" will remove all gaps in the input sequences, whereas setting removeGaps to "common" will remove only gaps that exist in the same position in every sequence. Therefore, the latter method will leave gaps in place that are not shared by every sequence, requiring that the sequences in myXStringSet all be the same length (i.e., be aligned). Setting removeGaps to "none" will simply return myXStringSet unaltered.

Value

An XStringSet of the same type as myXStringSet.

Author(s)

Erik Wright [e-mail]

See Also

AlignSeqs

Examples

dna <- DNAStringSet(c("ACT-G-", "AC--G-"))
dna
RemoveGaps(dna, "all")
RemoveGaps(dna, "common")

Example output

Loading required package: 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, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, 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

Loading required package: RSQLite
DNAStringSet object of length 2:
    width seq
[1]     6 ACT-G-
[2]     6 AC--G-
DNAStringSet object of length 2:
    width seq
[1]     4 ACTG
[2]     3 ACG
DNAStringSet object of length 2:
    width seq
[1]     4 ACTG
[2]     4 AC-G

DECIPHER documentation built on Nov. 8, 2020, 8:30 p.m.