defineClusters: Polycistronic clustering of miRNAs

In LXQin/DANA: Data-driven Normalization Assessment for miRNA-Seq Data

Polycistronic clustering of miRNAs

Description

Defines polycistronic clusters for a given set of miRNAs based on their chromosomal location. For microRNAs on the human genome (homo sapiens) using mirBAse v22 notation, chromosomal coordinates are provided. These can be used e.g. for data from TCGA. If you use miRNA annotation different from miRBase v22, you must provide your own chromosomal location including chromosome ('chr') and nucleotide position on the chromosome ('pos').

Usage

defineClusters(genes, chr, pos, threshold = 10000, ...)

Arguments

genes	List of genes for which the miRNA clustering is computed.
chr	Optional. Vector that specifies the chromosome for each miRNA in genes. If not given, miRBase v22 chromosomal coordinates is used.
pos	Optional. Vector of the nucleotice (base-pair) position of each miRNA in genes on its chromosome, which is specified in chr. This position could be e.g. the start, end or averaged ((start+end)/2) base-pair position on the associated chromosome. If not given, miRBase v22 chromosomal coordinates is used.
threshold	Maximum distance threshold in base-pairs for the difintion of polycistronic clusters. Default is 10,000, which corresponds to miRBase's cluster definition.

Value

Vector of clusters. Associates each miRNA in genes to a polycistronic cluster.

LXQin/DANA documentation built on March 7, 2024, 3:24 a.m.