alt_X_ranks: alt_left_ranks and alt_right_ranks functions: Identification...

In wokai/spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

Description

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.

Usage

alt_left_ranks(x)

Arguments

x	gapSites. Object for which alternative ranks are calculated

Details

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.

Value

data.frame. The table contains the columns nr_alt, alt_id, id, diff_ranks and gap_diff.

Author(s)

Wolfgang Kaisers

Examples

# 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)

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