CoreMicrobiomeR (version 0.1.0)

significance: 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)

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

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

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