MAGNAMWAR (version 2.0.4)

AnalyzeOrthoMCL: Main OrthoMCL Analysis

Description

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

Usage

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)

Arguments

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

Value

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

# NOT RUN {
#Linear Model

# }
# NOT RUN {
mcl_mtrx <- AnalyzeOrthoMCL(after_ortho_format, pheno_data, 'lm',
 'Treatment', resp='RespVar')
# }
# NOT RUN {
# the rest of the examples are not run for time's sake
#Linear Mixed Effect with one random effect
# }
# NOT RUN {
mcl_mtrx <- AnalyzeOrthoMCL(after_ortho_format, pheno_data, 'lmeR1',
'Treatment', resp='RespVar', rndm1='Experiment')
# }
# NOT RUN {

#Linear Mixed Effect with two independent random effects
# }
# NOT RUN {
mcl_mtrx <- AnalyzeOrthoMCL(after_ortho_format, pheno_data, 'lmeR2ind',
 'Treatment', resp='RespVar', rndm1='Experiment', rndm2='Vial')
# }
# NOT RUN {

#Linear Mixed Effect with rndm2 nested in rndm1
# }
# NOT RUN {
mcl_mtrx <- AnalyzeOrthoMCL(after_ortho_format, pheno_data, 'lmeR2nest',
 'Treatment',  resp='RespVar', rndm1='Experiment', rndm2='Vial')
# }
# NOT RUN {

#Linear Mixed Effect with two independent random effects and one additional fixed effect
# }
# NOT RUN {
mcl_mtrx3 <- AnalyzeOrthoMCL(after_ortho_format, pheno_data, 'lmeF2',
 'Treatment', resp='RespVar', fix2='Treatment', rndm1='Experiment', rndm2='Vial', princ_coord = 4)
# }
# NOT RUN {

#Wilcoxon Test
# }
# NOT RUN {
mcl_mtrx <- AnalyzeOrthoMCL(after_ortho_format, pheno_data, 'wx',
 'Treatment', resp='RespVar')
# }
# NOT RUN {
# ~ 5 minutes
#Survival with two independent random effects, run on multiple cores
# }
# NOT RUN {
mcl_mtrx <- AnalyzeOrthoMCL(after_ortho_format, starv_pheno_data, 'TRT', model='survmulti',
 time='t2', event='event', rndm1='EXP', rndm2='VIAL', multi=1)
# }
# NOT RUN {
# ~ 5 minutes
#Survival with two independent random effects and one additional fixed effect,
#including drops on multi cores
# }
# NOT RUN {
mcl_mtrx <- AnalyzeOrthoMCL(after_ortho_format, starv_pheno_data, 'TRT', model='survmulticensor',
 time='t1', time2='t2', event='event', rndm1='EXP', rndm2='VIAL', fix2='BACLO', multi=1)
 
# }
# NOT RUN {
#to be appended with SurvAppendMatrix
# }