gapSites-class: Class '"gapSites"': Container for tabulated alignment gap...

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

Description

Contains tabulated data on alignment gaps on RNA - seq data. "getalignGaps(reader,seqid)" reads gapped alignments for the specified seqid from a BAM file (via CRAN rbamtools) into an object of class "gapSites".

Objects from the Class

Objects can be created by calls of the form alignGapList(reader).

Slots

nAligns:

Object of class "numeric" Total number of aligns in alignment.

nAlignGaps:

Object of class "numeric" Total number of gapped aligns in alignment.

dt:

Object of class "data.frame" Table containing basic data for object.

annotation:

Object of class "dataFrameOrNULL" Optional data.frame containing annotation data.

profile:

dataFrameOrNULL Optional. Contains probe information (Name of BAM-file, group affiliation, number of sites).

Methods

as.data.frame

signature(x = "gapSites"): Returns copy of contained data.frame.

c

signature(x = "gapSites"): Specialisation of generic combine function.

dim

signature(x = "gapSites"): Specialisation of generic dim function.

dnaGapSites

signature(x = "gapSites", dnaset="DNAStringSet"): Create dnaGapSites object by adding DNA sequences.

getAnnStrand

signature(x): Return strand vector based on annotation content.

getProfile

signature(x): Return profile table (data.frame) which contains BAM-file names, group affiliation and number of Sites.

gptm

signature(x = "gapSites"): Reading accessor for gptm values.

head

signature(x = "gapSites"): Specialisation of generic head function.

lrCodons

signature(x = "gapSites"): Returns gapSites object where lstart and rend positions are truncated toward the next smaller full codon position (used for preparation of translation to amino acid sequence)

lJunc

signature(x = "gapSites", featlen="numeric", gaplen="numeric", keepStrand="logical" (FALSE), unique="logical" (FALSE)): featlen: Number nucleotides of feature (=exon). gaplen: Number of nucleotides of gap (=intron). keepStrand: Values for strand are copied from argument, otherwise all positions are marked as "+". unique: Multiple identical positions (arising from alternative splice sites on the right side) are collapsed to one line (number of sites is counted in "mult"). Position: 0-based position of last exon nucleotide in DNA sequence.

lrJunc

signature(x = "gapSites", lfeatlen="numeric", rfeatlen="numeric", "strand"): Returns gapSites object where positions are shifted so that given feature length's are present for lstart and rend positions (used as preparatory steps for obtaining sensible seq - logo's on exonic junction regions).

addGeneAligns

signature(object="gapSites"): Adds number of alignments per gene as new column to alignment gap position table. Annotation tables must be present. Otherwise an error occurs.

merge

signature(x = "gapSites", y = "ANY"): Specialisation of generic merge (data.frame) function.

nAligns

signature(object = "gapSites"): Reading accessor for nAligns value.

nAlignGaps

signature(object = "gapSites"): Reading accessor for nAlignGaps value.

rpmg

signature(x = "gapSites"): Reading accessor for rpmg values.

show

signature(object = "gapSites"): Specialisation of generic show function.

sortTable

signature(x="gapSites"): Sorts all contained tables by seqid, lend and rstart.

write.annDNA.tables

signature(x="gapSites", dnaset="DNAStringSet", filename="character", featlen="numeric", gaplen="numeric", sep="character", dec="character", row.names="logical"): Writes csv file with gap-positions, annotations and dna-sequence.

Author(s)

Wolfgang Kaisers

See Also

dnaGapSites

Examples

bam<-character(2)
bam[1]<-system.file("extdata","rna_fem.bam",package="spliceSites")
bam[2]<-system.file("extdata","rna_mal.bam",package="spliceSites")
reader<-bamReader(bam[1],idx=TRUE)
agl<-alignGapList(reader)
agl
bamClose(reader)

mbs<-readMergedBamGaps(bam)
mbs
getProfile(mbs)

wokai/spliceSites documentation built on May 4, 2019, 9:46 a.m.