seqlogo: seqlogo: Plotting sequence logo for 'cdRanges' and...

In spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

Description

The function produces a sequence logo plot based on the contained sequences.

Usage

seqlogo(x,strand="+",useStrand=TRUE,...)

Arguments

x	cdRanges or dnaGapSites Object.
strand	Character. Determines the subset for which the seqlogo is plotted. This option is only used when useStrand is given as 'TRUE'.
useStrand	Logical. Determines whether the given strand information is used. For useStrand=FALSE the plot is made up from all contained sequences.
...	(Currently unused)

Details

The function fails with an error message when the dataset does not contain any records with the given strand (except useStrand=FALSE).

Value

None

Author(s)

Wolfgang Kaisers

Examples

bam<-system.file("extdata","rna_fem.bam",package="spliceSites")
reader<-bamReader(bam,idx=TRUE)
ga<-alignGapList(reader)
bamClose(reader)
lj<-lJunc(ga,featlen=6,gaplen=6,strand='+')
dnafile<-system.file("extdata","dna_small.RData",package="spliceSites")
load(dnafile)
ljd<-dnaRanges(lj,dna_small)
seqlogo(ljd)

Example output

Loading required package: rbamtools
Loading required package: refGenome
Loading required package: doBy
Loading required package: RSQLite
Loading required package: Biobase
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

Welcome to Bioconductor

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

Loading required package: Biostrings
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

[dnaRanges.cRanges] Removing 0 rows from cRanges due to unknown strand (rest: 46 rows).
[dnaRanges.cRanges] Reversed 0 sequences.
[seqlogo.cdRanges]  + : 46, total: 46.

spliceSites documentation built on May 6, 2019, 3:05 a.m.