clean: Remove sequences with ambiguous nucleotides from short read...

In ShortRead: FASTQ input and manipulation

Description

Short reads may contain ambiguous base calls (i.e., IUPAC symbols different from A, T, G, C). This generic removes all sequences containing 1 or more ambiguous bases.

Usage

clean(object, ...)

Arguments

object	An object for which clean methods exist; see below to discover these methods.
...	Additional arguments, perhaps used by methods.

Details

The following method is defined, in addition to methods described in class-specific documentation:

clean

signature(x = "DNAStringSet"): Remove all sequences containing non-base (A, C, G, T) IUPAC symbols.

Value

An instance of class(object), containing only sequences with non-redundant nucleotides.

Author(s)

Martin Morgan <[e-mail]>

Examples

showMethods('clean')

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: BiocParallel
sh: 1: cannot create /dev/null: Permission denied
sh: 1: wc: Permission denied
'BiocParallel' did not register default BiocParallelParams:
  missing value where TRUE/FALSE needed
Loading required package: Biostrings
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: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Function: clean (package ShortRead)
object="DNAStringSet"
object="ShortRead"

Warning message:
system call failed: Cannot allocate memory 

ShortRead documentation built on Nov. 8, 2020, 8:02 p.m.