alt_X_ranks {spliceSites} | R Documentation |
alt_X_ranks covers the functions alt_left_ranks
and
alt_right_ranks
.
Both functions identify alternative splice-sites.
alt_left_ranks
finds sites which share the same rstart
value
(on the same seqid).
alt_right_ranks
finds sites which share the same lend
value
(on the same seqid).
alt_ranks
combines the results of both functions together wich
seqid
, lend
and rstart
values in one table.
alt_left_ranks(x)
x |
gapSites. Object for which alternative ranks are calculated |
The function alt_left_ranks
groups align-gaps (splice-sites)
which share identical rstart
position and have different lend
position.
Each Group is assigned a unique alt_id
(integer value beginning from 1).
The first column in the returned data.frame is an id-column which facilitates
table merging with the source table.
The result has the same number of rows as the source and the id-column.
data.frame. The table contains the columns nr_alt, alt_id, id, diff_ranks and gap_diff.
Wolfgang Kaisers
# A) Read gapSites bam<-system.file("extdata","rna_fem.bam",package="spliceSites") reader<-bamReader(bam,idx=TRUE) ga<-alignGapList(reader) bamClose(reader) # B) alt_ranks alr<-alt_left_ranks(ga) ar<-alt_ranks(ga)