rbamtools (version 2.16.17)

bamGapList-class: 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.

Examples

# NOT RUN {
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)
# }