dnaRanges: Reads a bamRange object for a given 'bamReader', 'refGenome'...

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

Description

Locates gene in genome via refGenome and reads a bamRange from the determined region.

Usage

dnaRanges(x,dnaset,useStrand=TRUE,removeUnknownStrand=TRUE,verbose=TRUE,...)

Arguments

x	cRanges. Range-data will be copied from this object.
dnaset	DNAStringSet. Contains the reference sequence from which the DNA-sequence is extracted.
useStrand	logical. When TRUE, sequences for which strand='-' are reverse-complemented.
removeUnknownStrand	logical. When TRUE, sequences for which strand='-' are removed.
verbose	logical. Determines amount of console output during routine runtime.
...	Optional additional arguments (currently unused).

Value

cdRanges

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.