Description Usage Arguments Value
View source: R/AnalyzeOrthoMCL.R
Main function for analyzing the statistical association of OG (orthologous group) presence with phenotype data
1 2 3 4 |
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
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