RaceID (version 0.3.9)

maxNoisyGenesTB: Function for extracting genes maximal variability

Description

This function extracts genes with maximal variability in a cluster or in the entire data set.

Usage

maxNoisyGenesTB(noise, cl = NULL, set = NULL, minobs = 5)

Value

Vector with average gene expression variability in decreasing order, computed across all cells or only cells in a set of clusters (if cl and set are given.

Arguments

noise

List object with noise parameters returned by the compTBNoise function.

cl

List object with clustering information, returned by the graphCluster function. Default is NULL.

set

Postive integer number or vector of integers corresponding to valid cluster numbers. Noise levels are computed across all cells in this subset of clusters. Default is NULL and noise levels are computed across all cells.

minobs

Positive integer number. Only genes with at least minobs neighbourhoods with non-zero biological noise levels in set are included. Default is 5.

Examples

res <- pruneKnn(intestinalDataSmall,knn=10,alpha=1,no_cores=1,FSelect=FALSE)
noise <- compNoise(intestinalDataSmall,res,pvalue=0.01,genes = NULL,no_cores=1)
mgenes <- maxNoisyGenes(noise)