clusterOn: Check expression of a given feature against clinical variable

In Bioconductor/MultiOmicQC: Quality control for Multi-omics datasets

Description

Function that outputs a DataFrame with participant ID, sample ID, the select colData column, the expression values for select rownames, and the center values for each gene by cluster.

Usage

clusterOn(MultiAssayExperiment, colDataCols, rownames, experiments,
  seed = NULL)

Arguments

MultiAssayExperiment	A MultiAssayExperiment object
colDataCols	Select columns from the MultiAssayExperiment colData DataFrame
rownames	Features to be used for clustering (e.g., a set of gene names)
experiments	A character vector indicating assays of interest in the ExperimentList
seed	A single integer value passed to set.seed (default NULL)

Value

A DataFrame with appended cluster and center values

Examples

library(MultiAssayExperiment)
example(MultiAssayExperiment)
clusterOn(myMultiAssayExperiment, colDataCols = "sex",
    rownames = c("XIST", "RPS4Y1", "KDM5D"),
    experiments = "RNASeqGene", seed = 42L)

Bioconductor/MultiOmicQC documentation built on May 22, 2019, 12:59 p.m.