rbamtools (version 2.16.17)

gapSiteList-class: 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.

Examples

# NOT RUN {
# 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()
# }