R: Class '"gapList"': Representation of genomic alignment gaps.

gapList-class {rbamtools} | R Documentation

## Class `"gapList"`: Representation of genomic alignment gaps.

### Description

The gapList class represents a list of Alignment gaps (i.e. N-items in Cigar-data). For each gap, the type of left and right adjacent Cigar items is reported plus size of each. The list can be converted into a data.frame which then contains the columns: refid, position (which identify the align), left_cigar_len,left_cigar_type, left_stop (characterize the left boundary) and right_start, right_cigar_len, right_cigar_type (characterize the right boundary). The adjacent cigar-types should be 0 (i.e. M=match). 'left_stop' is the 0-based position of last exon nucleotide, right_start is the 0-based position of the first exon nucleotide.

### Objects from the Class

Objects can be created by calls of the form `gapList(reader,coords))`.

### Slots

`list`:

  `"externalptr"`. Point to double linked list struct.

### Methods

size

  `signature(x="gapList")`: Returns number of gapped-align items in list.

coerce

  `signature(from="gapList", to="data.frame")`: Coercion of gapList to data.frame.

as.data.frame

  `signature(x="gapList", row.names=NULL, optional=FALSE)`: Coercion of gapList to data.frame.

show

  `signature(object="gapList")`: Prints a short message with some summarizing data.

nAligns

  `signature(object="gapList")`: Returns number of aligns in specified Range.

nAlignGaps

  `signature(object="gapList")`: Returns number of align gaps in specified Range.

### Author(s)

Wolfgang Kaisers

### Examples

    # Open (indexed) BAM file
    bam<-system.file("extdata", "accepted_hits.bam", package="rbamtools")
    reader<-bamReader(bam,idx=TRUE)
    coords<-getRefCoords(reader,"chr1")
    gl<-gapList(reader,coords)
    size(gl)
    nAligns(gl)
    nAlignGaps(gl)
    gl
    dfr<-as.data.frame(gl)
    # coerce
    dfr<-as(gl,"data.frame")
    head(df)
    bamClose(reader)

[Package rbamtools version 2.16.17 Index]