get.gene.coexpression.space: get.gene.coexpression.space

In seriph78/COTAN_stable: COexpression Tables ANalysis

Description

To make the GDI more specific, it may be desirable to restrict the set of genes against which GDI is computed to a selected subset V with the recommendation to include a consistent fraction of cell-identity genes, and possibly focusing on markers specific for the biological question of interest (for instance neural cortex layering markers). In this case we denote it as local differentiation index (LDI) relative to V.

Usage

get.gene.coexpression.space(object, n.genes.for.marker = 25, primary.markers)

## S4 method for signature 'scCOTAN'
get.gene.coexpression.space(object, n.genes.for.marker = 25, primary.markers)

Arguments

object	The COTAN object.
n.genes.for.marker	The number of genes correlated with the primary markers that we want to consider. By default this is 25.
primary.markers	A vector of primary marker names.

Value

A dataframe

Examples

data("ERCC.cotan")
df = get.gene.coexpression.space(ERCC.cotan, n.genes.for.marker = 10,
primary.markers=rownames(ERCC.cotan@raw[sample(nrow(ERCC.cotan@raw),5),]))

seriph78/COTAN_stable documentation built on Dec. 23, 2021, 12:19 a.m.