alt_X_ranks {spliceSites} | R Documentation

## alt_left_ranks and alt_right_ranks functions: Identification of alternative splicing events from gapped alignments.

### 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)

[Package spliceSites version 1.30.0 Index]