spliceSites-package: Calculate information on splice-sites from gapped alignments...

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

Description

The package defines 'cRanges' the (centered ranges) class which represents a genomic range that contains a highlighted position (center): This will usually be the boundary between an exon and an intron. The second defined type is the class 'gapSites' which represents two exonic regions divided by a gap (usually an intron). There are subclasses which additionally contain DNA or AA sequences.

Details

Package:	spliceSites
Type:	Package
Version:	1.0
Date:	2012-10-28
License:	GPL-2
Depends:	methods,rbamtools,refGenome,Biobase,BiocGenerics,Biostrings,seqLogo

Author(s)

Wolfgang Kaisers Maintainer: Wolfgang Kaisers <[e-mail]>

References

Yeo G, Burge CB Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 2004; 11(2-3):377-94 http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html

See Also

rbamtools refGenome

Examples

bam <- system.file("extdata", "rna_fem.bam", package="spliceSites")
reader <- bamReader(bam, idx=TRUE)
ga <- alignGapList(reader)
bamClose(reader)
dnafile <- system.file("extdata", "dna_small.RData", package="spliceSites")
load(dnafile)
ucf <- system.file("extdata","uc_small_junc.RData", package="spliceSites")
ucj <- loadGenome(ucf)
annotation(ga) <- annotate(ga, ucj)
ga

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

[overlapJuncs] Input preparation.
[overlapJuncs] Query size          :        46	Ref  size :        172
[overlapJuncs] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[overlapJuncs] i:  1	seqid: chr1	query set:      32	ref set:   129
[overlapJuncs] i:  2	seqid: chr16	query set:       2	ref set:     2
[overlapJuncs] i:  3	seqid: chr6	query set:      11	ref set:    18
[overlapJuncs] i:  4	seqid: chrY	query set:       1	ref set:    23
[overlapJuncs] Result assemly.
[overlapJuncs] Finished.
[annotate.gapSites] Finished.
Object of class gapSites with 46 rows and 16 columns.
nAligns:  3107 	nAlignGaps:  3368 
  id seqid lstart  lend rstart  rend gaplen nAligns nProbes nlstart qsm nmcl
1  1  chr1  14730 14829  14970 15052    140     553       1       8 200    8
2  2  chr1  14944 15038  15796 15888    757     201       1       8 181    8
3  3  chr1  15909 15947  16607 16702    659      29       1       8 115    8
4  4  chr1  15953 16027  16607 16669    579       4       1       4 138    4
5  5  chr1  16730 16765  16854 16941     88       5       1       5  95    5
6  6  chr1  16682 16765  16858 16957     92      34       1       8 172    8
   gqs strand       gptm       rpmg    gene_id gene_name
1 1000      * 1779851.95 164192.399 uc001aac.4    WASH7P
2  905      *  646926.30  59679.335 uc009vis.3    WASH7P
3  575      *   93337.62   8610.451 uc009vix.2    WASH7P
4  345      *   12874.16   1187.648 uc009vix.2    WASH7P
5  296      *   16092.69   1484.561 uc009viz.2    WASH7P
6  860      *  109430.32  10095.012 uc009viv.2    WASH7P
Warning message:
system call failed: Cannot allocate memory 

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