ClusterExons: Detect constitutive and alternative exons

In alfredorago/FESTA: Flexible Exon-based Splicing and Transcription Annotation

Description

Cluster genes according to reciprocal correlations, then iteratively cut tree (bottom up) until one cluster is the most expressed or tied for expression across all samples. Uses hcluster from amap package for clustering

Usage

ClusterExons(data = NULL, exonID = NULL, exceptions = ceiling(ncol(data) *
  0.1), signDigits = 3, distMethod = "correlation", link = "complete",
  nbproc = 1)

Arguments

data	A data.frame or numeric matrix with one row per exon and one column per sample, containing the expression values of each exon.
exonID	A data.frame with the following columns. geneID Gene ID of each exon. exonID ID of each exon.
exceptions	Integer. Sets the maximum number of samples in which the constitutive exon group does not need to be the most expressed one. Defaults to 10% of the dataset.
signDigits	An integer. Number of digits rounded from expression scores for ranking calculations.
distMethod	The distance metric used by the clustering algorithm (default: correlation), see function hcluster from package amap for more information.
link	Agglomeration method used by the clustering algorithm (default: complete), see function hcluster from package amap for more information.
nbproc	Integer. Number of subprocess for parallelization (default: 1), see function hcluster from package amap for more information

Value

A data.frame with the following columns.

geneID

Gene ID of each exon.

clusters

Numeric ID for each exon group detected.

exonID

Exon ID.

splicing_category

Gene class. Can be either spliced (isoforms detected), unspliced (no isoforms detected) or single_expressed_exon (only one exon present in the gene).

constitutive

Identifies whether the exon group is constitutive (main gene) or facultative (isoform).

transcriptID

Identifier for each exon group detected. Ends in '_con' for constitutive and '_fac' for facultative exons.

Examples

 ExonAssignment = ClusterExons(data = SIRV_data$tpm, exonID = SIRV_data$ID)

alfredorago/FESTA documentation built on May 24, 2019, 9:50 a.m.