jinhao94 / omics

Robust association network construction between any two omics data type, including fecal microbial MGSs

Description

This script is used to find associations between any two omics data, including clinical metadata and potentially high-dimensional omics data, by a cross validation function for random forest.

Usage

R omics.R omics_input1 omics_input2 out.prefix

• omics_input1

  It is required to be in csv format. Rows represent samples, and columns represent metadata or features.

  Here is an example:

	BMI	Age	Hip_circumference
Sample1	20	26	83.2
Sample2	19	30	90.2
Sample3	27	32	82.5
Sample4	18	28	NA

• omics_input2

  The format of omics_input2 is the same as omics_input1.

• out.prefix

  Specify the prefix of output file.

Output files

The following files will be generated after the analysis.

• $out.prefix.imp_omics.csv

  This file shows the RFCV importance.

• $out.prefix.crsq_omics.csv The meaning of each column in this file is as followed:

   "var" : Variable names
   "cut": Best number of predictors used in the model
   "sample": Shared sample numbers of target and predict dataset
   "n.var": Same as original rfcv, that is number of varialbes used in the model
   "error.cor": Spearman correlation between prediction and true measurments
   "error.nmse": Normalized MSE (NMSE), also known as Normalized Ensemble Variance (NEV)
   "error.r2": Same as original rfcv, that is rsqure.
   "error.mape": Mean Absolute Percentage Error (MAPE) 
   "error.mse": Mean Squared Error Mean Squared Error, or MSE for short
   "error.mae": Mean Absolute Error (MAE), which measures the average magnitude of the errors in a set of predictions, without considering their direction
   "error.MedianAE": Median absolute error
   "error.RAE": Relative Absolute Error (RAE)
   "error.RMSE": The Root Mean Squared Error, or RMSE
  

• $out.prefix.pred_omics.csv

  Represents the result for RFCV prediction.

Notice

You should specify the path where input files(eg, omics_input2 and omics_input1) locate in the script line 135 and line 141.