In tkostas/komics: Tools to analyze omics data

Identify groups
Perform ANOVA test and extract p-values
Correct p-values for multiple hypothesis testing error

# e.g. define a vector with the sample names. You can extract it directly using names(my_data)
sample_names <- c("A01", "A02", "A03",
                  "B01", "B02", "B03", 
                  "C01", "C02", "C03")


# Define a second vector with the group names, keeping the same order with above
group_names <- c("A", "A", "A",
                 "B", "B", "B", 
                 "C", "C", "C")

# Merge both vectors in one dataframe in case that you need to exclude groups etc
sample_groups <- data.frame(samples = sample_names, groups = group_names)


# Calculate pvalues. No-pairwise comparison is performed. If there is sigificant difference
# it is across the complete set.
processed_data <- calc_aov_padj(x = my_data, 
                                sample_names = sample_groups$samples, 
                                group_names = sample_groups$groups,
                                pAdj = "BH") # see ?p.adjust for more options