AnalyzeOrthoMCL: Main OrthoMCL Analysis
In corinsexton/MAGNAMWAR: A Pipeline for Meta-Genome Wide Association

Main function for analyzing the statistical association of OG (orthologous group) presence with phenotype data

AnalyzeOrthoMCL(mcl_data, pheno_data, model, species_name, resp = NULL,
  fix2 = NULL, rndm1 = NULL, rndm2 = NULL, multi = 1, time = NULL,
  event = NULL, time2 = NULL, startnum = 1, stopnum = "end",
  output_dir = NULL, sig_digits = NULL, princ_coord = 0)

`mcl_data`	output of FormatAfterOrtho; a list of matrices; (1) a presence/absence matrix of taxa per OG, (2) a list of the specific protein ids within each OG
`pheno_data`	a data frame of phenotypic data with specific column names used to specify response variable as well as other fixed and random effects
`model`	linear model with gene presence as fixed effect (lm), linear mixed mffect models with gene presence as fixed effect and additional variables specified as: one random effect (lmeR1); two independent random effects (lmeR2ind); two random effects with rndm2 nested in rndm1 (lmeR2nest); or two independent random effects with one additional fixed effect (lmeF2), Wilcox Test with gene presence as fixed effect (wx), Survival Tests with support for multi core design: with two random effects (survmulti), and with two times as well as an additional fixed variable (survmulticensor)
`species_name`	Column name in pheno_data containing 4-letter species designations
`resp`	Column name in pheno_data containing response variable
`fix2`	Column name in pheno_data containing second fixed effect
`rndm1`	Column name in pheno_data containing first random variable
`rndm2`	Column name in pheno_data containing second random variable
`multi`	(can only be used with survival tests) Number of cores
`time`	(can only be used with survival tests) Column name in pheno_data containing first time
`event`	(can only be used with survival tests) Column name in pheno_data containing event
`time2`	(can only be used with survival tests) Column name in pheno_data containing second time
`startnum`	number of test to start on
`stopnum`	number of test to stop on
`output_dir`	(if using survival tests) directory where small output files will be placed before using SurvAppendMatrix. Must specify a directory if choosing to output small files, else only written as a matrix
`sig_digits`	amount of digits to display for p-values and means of data; default to NULL (no rounding)
`princ_coord`	the number of principle coordinates to be included in model as fixed effects (1, 2, or 3), if a decimal is specified, as many principal coordinates as are needed to account for that percentage of the variance will be included in the analysis

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

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