reCluster: Adjusting the cluster.

In BMILAB/AStrap: Identificantion of alternative splicing events and classificaiton of alternative splicing types

Description

To obtain all potential clusters with more than one isoform for further analysis, a second-round mapping can be performed on clusters with single isoform. Isoforms passing the second-round mapping were reassigned to the .

Usage

reCluster(Align, cdhit.result, re.id = 0.7, re.co = 0.7)

Arguments

Align	A data frame contation the information of sequence alignments.
cdhit.result	A data frame holds isoform clusters.
re.id	An numeric value indicating the threshold of identity of alignment for the second-round mapping (default: 0.7). Used only if recluster = TRUE.
re.co	An numeric value indicating the threshold of coverage of alignment for the second-round mapping (default: 0.7). Used only if recluster = TRUE.

Value

A list contation the pairwise sequence alignments in a cluster, including two elements: alignment and cluster. alignment is a data frame storage the pairwise alignment of isoform in a cluster; cluster is a data frame storage the new clustering result after second-round mapping.

Examples

##Loading the example data
load(system.file("data","example_recluster.Rdata",package = "AStrap"))
result <- reCluster(gmap.align,cdhit.result,re.id=0.7,re.co=0.7)

BMILAB/AStrap documentation built on Nov. 20, 2020, 4:03 p.m.