CorAnalysisDataset: CorAnalysisDataset:

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

Description

Correlates every gene in a dataset with every other gene in the same dataset. Allows a timelag between genes to be correlated.

Usage

CorAnalysisDataset(
  dataset,
  average = "median",
  lag = 0,
  nthreads = NULL,
  save = TRUE,
  filename = NULL
)

Arguments

dataset	A transcriptomics dataset. First columns should be gene names. All other columns should be expression levels.
average	The average to be used when comparing the time points. Either 'median' or 'mean'.
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 genes whilst the rows represent lagged genes.

Examples

cordf <- CorAnalysisDataset(Laurasmappings, lag=1, nthreads = 2,
                            filename='cor_tfiltered')

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