gapSiteList-class: Class '"gapSiteList"': Representation of genomic alignment...

In wokai/rbamtools: An R package for reading and writing BAM (Binary alignment) files.

Description

The gapList 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.

Methods

size

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

coerce

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

coerce

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

refID

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

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)
bamClose(reader)

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