gapSites-class {spliceSites} | R Documentation

## Class `"gapSites"`: Container for tabulated alignment gap positions on 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)

[Package spliceSites version 1.28.0 Index]