significance {CoreMicrobiomeR}

Testing the Significance of the Identified Core Microbiome

Description

This function performs a two-sample variance test to assess the statistical significance of differences in abundance between core OTUs and non-core OTUs. It takes two data frames as input, representing the abundance of core OTUs and non-core OTUs, and returns the results of the variance test. It tells whether the identified core represents the particular environment or habitat.

Usage

significance(core_ids, non_core_ids)

Arguments

core_ids

A Dataframe of core OTUs where the first row is the OTU ID and column names refer to sites/sample names

non_core_ids

A Dataframe of non_core OTUs where the first row is the OTU ID and column names refer to sites/sample names

Value

This function gives the list which consist of following results.

'statistic' Calculated F test statistic

'parameter' The numerator degrees of freedom (num df), and the denominator degrees of freedom (denom df)

'p-value' Probability value

'alternative' The alternative hypothesis for this test is that the true ratio of variances is not equal to 1. This suggests that the variances of the two data sets are different

'conf.int' 95 percent confidence interval limit for the ratio of variances

'estimate' Ratio of variances between core_data and non_core_data calculated

'method' The test performed is an F test, which compares the variances of the two data sets

'data.name' The data used for the test are core_ids and non_core_ids

Examples

#To run input data
core_1 <- CoreMicrobiome(
 otu_table = demo_otu,
 tax_table = demo_tax,
 metadata_table = demo_md,
 filter_type = "occupancy_fun_filter", #Or "abundance_fun_filter", Or "combined_filter"
 percent = 0.5,
 method = "css",  # Or "srs", "rrarefy", "tmm", "tmmwsp", "rle", "upperquartile", "none"
 beta_diversity_method = "jaccard",
 top_percentage = 10  # Adjust the percentage as needed for core/non-core OTUs
)
#To run significance test
f_test <- significance(core_1[["core_otus"]] , core_1[["non_core_otus"]] )

#To view the significance test result
f_test