Description Objects from the Class Slots Methods Author(s) Examples
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 can be created by calls of the form siteList(reader,coords))
.
list
:"externalptr"
. Point to double linked list struct.
signature(x = "gapList")
:
Returns number of site-items in list.
signature(from = "gapList", to = "data.frame")
:
Coercion of gapSiteList to data.frame.
signature("gapList","data.frame")
:
Coercion of gapSiteList to data.frame.
signature(object = "gapList")
:
Prints a short message with some summarizing data.
signature(object = "gapList")
:
Returns number of aligns in specified Range.
signature(object = "gapList")
:
Returns number of align gaps in specified Range.
signature(object="gapList")
:
Returns refID from which gapList
has been retrieved.
Wolfgang Kaisers
1 2 3 4 5 6 7 8 9 10 11 12 13 | # 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.