R: Class '"bamGapList"'

bamGapList-class {rbamtools} | R Documentation

## Class `"bamGapList"`

### Description

The bamGapList class represents a list of Alignment gap (N-items in Cigar-data) sites . For each gap-site, left and right start and end positions as well as the gap-length are reported. Numbers of aligns supporting this site, number of left-sided start positions (<= 8) and the sum of overlapping nucleotides on the left side are given.

### Objects from the Class

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

### Slots

`list`:

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

`refdata`:

  `"data.frame"`. Contains bamHeader like data for stored aligns.

### Methods

size

  `signature(x = "bamGapList")`: Returns number of site-items in list.

coerce

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

coerce

  `signature("bamGapList","data.frame")`: Coercion of bamGapList to data.frame.

show

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

nAligns

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

nAlignGaps

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

### Author(s)

Wolfgang Kaisers

### Examples

    library(rbamtools)
    bam<-system.file("extdata", "accepted_hits.bam", package="rbamtools")
    reader<-bamReader(bam,idx=TRUE)
    bsl<-bamGapList(reader)
    bsl
    size(bsl)
    nAligns(bsl)
    nAlignGaps(bsl)
    summary(bsl)
    dfr<-as.data.frame(bsl)
    head(dfr)
    bamClose(reader)

[Package rbamtools version 2.16.17 Index]