network_calc: Calculates Correlations

In pmartR/pmartRseq: Analysis and Visualization of 16S Data

Description

This function calculates correlations for use in network analysis.

Usage

network_calc(omicsData, type = "spearman", group = FALSE,
  group_var = NULL, fdr_method = "fndr", missing_val = 0)

Arguments

omicsData	an object of the class 'seqData' reated by as.seqData.
type	Character, which correlation metric to use. Must be one of 'pearson' or 'spearman'. Default is 'spearman'.
group	Logical, should correlation analysis be performed on sub-groups of the data. Default is FALSE, will use all of the samples in the data.
group_var	Character, if group==TRUE, which variable to use as the grouping variable.
fdr_method	a character vector stating which cutoff method to use, one of 'fndr', 'pct0', or 'locfdr'. Default is 'fndr'.
missing_val	Use 0 or NA for any 'missing' values? Default is 0.

Details

Correlation is calculated between every pair of features.

Value

An object of class corrRes (also a data.frame) containing the correlation values.

Author(s)

Allison Thompson

Examples

## Not run: 
library(mintJansson)
data(rRNA_data)
mynetwork <- network_calc(omicsData = rRNA_data)
head(mynetwork)

## End(Not run)

pmartR/pmartRseq documentation built on May 25, 2019, 9:20 a.m.