do_wgcna: do_wgcna

In kuppal2/xmsPANDA: R Package for Biomarker Discovery, Network, and Data Exploratory Analysis

Description

This function performs module preservation analysis using WGCNA.

Usage

do_wgcna(feature_table_file = NA, class_labels_file = NA, X = NA, 
Y = NA, sigfeats = NA)

Arguments

feature_table_file	Path and name of feature table that includes the mz, retention time, and measured intensity in each sample for each analyte. The first 2 columns should be the mz and time. The remaining columns should correspond to the samples in the class labels file with each column including the intensity profile of a sample. Full path required. Eg: C:/My Documents/test.txt The feature table should be in a tab-delimited format. An example of the input file is provided under the "example" folder.
class_labels_file	File with class labels information for each sample. Samples should be in the same order as in the feature table. Please use the same format as in the example folder. If you want to adjust for covariates in "lmreg" option, then you can add additional columns, one per covariate. Categorical variables should be strings (eg: "male", "female"). Please see "classlabels_gender.txt" file as an example.
X	R object for feature table. If this is given, then feature table can be set to NA.
Y	R object for response/class labels matrix. If this is given, then class labels file can be set to NA.
sigfeats	List of differentially expressed features. Default: NA

Details

This function calls WGCNA to perform module preservation analysis between different classes or groups.

Value

PDF plots for module preservation from WGCNA and preservation matrix

Author(s)

Karan Uppal

References

WGCNA (Horvath 2007)

kuppal2/xmsPANDA documentation built on May 15, 2021, 5:48 a.m.