SurvAppendMatrix: Append Survival Test Outputs

In corinsexton/MAGNAMWAR: A Pipeline for Meta-Genome Wide Association

Description

Function used to append all .csv files that are outputted from AnalyzeOrthoMCL into one matrix.

Usage

SurvAppendMatrix(work_dir, out_name = "surv_matrix.csv", out_dir = NULL)

Arguments

work_dir	the directory where the output files of AnalyzeOrthoMCL are located
out_name	file name of outputted matrix
out_dir	the directory where the outputted matrix is placed

Value

A csv file containing a matrix with the following columns: OG, p-values, Bonferroni corrected p-values, mean phenotype of OG-containing taxa, mean pheotype of OG-lacking taxa, taxa included in OG, taxa not included in OG

Examples

file <- system.file('extdata', 'outputs', package='MAGNAMWAR')
directory <- paste(file, '/', sep = '')
SurvAppendMatrix(directory)

corinsexton/MAGNAMWAR documentation built on May 13, 2019, 10:51 p.m.