CorAnalysisClusterDataset: CorAnalysisClusterDataset:

In nathansam/CircadianTools: Collection of Tools for Detecting Rhythmic Genes

Description

Correlates the average activity of each cluster with every other cluster in a dataset.

Usage

CorAnalysisClusterDataset(
  cluster.dataset,
  lag = 0,
  nthreads = NULL,
  save = TRUE,
  filename = NULL
)

Arguments

cluster.dataset	A transcriptomics dataset where the final column details the cluster the gene belongs to. First column should be gene names. All remaining columns should be expression levels.
lag	Setting any value other than 0 allows a gene to be correlated with lagged genes in the dataset. The number denotes the number of timesteps to lag by.
nthreads	The number of threads to be used for parallel computations. Defaults to the maximum number of threads available.
save	Logical. If TRUE, the dataframe of correlations for the dataset is saved as a .csv file.
filename	filename for saved csv file. Only used if save=TRUE. If not specified then the dataset object name is used.

Value

A dataframe of correlation values. The column genes represent the original clusters whilst the rows represent lagged clusters.

Examples

pam.df <- PamClustering(Laurasmappings, k = 10, nthreads = 2)
cor.df <- CorAnalysisClusterDataset(pam.df, nthreads = 2)

nathansam/CircadianTools documentation built on Dec. 26, 2019, 11:30 a.m.