R: Class '"gapSiteList"': Representation of genomic alignment...

gapSiteList-class {rbamtools} | R Documentation

## Class `"gapSiteList"`: Representation of genomic alignment gap positions.

### Description

The gapSiteList class represents pooled alignment-gap sites. Gap-sites are characterized by unique refid, left-end and right-start positions in each list. 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.

### Methods

size

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

coerce

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

coerce

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

show

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

nAligns

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

nAlignGaps

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

refID

  `signature(object="gapSiteList")`: Returns refID from which `gapSiteList` has been retrieved.

refID<-

  `signature(object="gap", value="numeric")`: Sets flag item.

### 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")
    sl<-siteList(reader,coords)
    size(sl)
    nAligns(sl)
    nAlignGaps(sl)
    sl
    refID(sl)
    df<-as.data.frame(sl)
    head(df)
    # Create from bamRange:
    br <- bamRange(reader, coords)
    sl <- siteList(br)
    #
    bamClose(reader)
    # Create empty list
    sl <- siteList()

[Package rbamtools version 2.16.17 Index]