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

Description Usage Arguments Details Value Author(s) Examples

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

1
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 <mtmorgan@fhcrc.org>

Examples

1
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.