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Remove Mock Features from a Phyloseq Object

Source: R/remove_mock.R
remove_mock.Rd

This function removes mock features from a phyloseq object. These mock features, which can appear in other samples due to cross-contamination, are removed to minimize their impact on the analysis samples. In addition, the function filters the dataset to retain only samples without controls. Users can choose whether to remove the mock features by setting the mock parameter.

Usage

remove_mock(physeq = decontam_physeq, mock_genera = mock_genera, mock = TRUE)

Arguments

physeq

A phyloseq object containing the microbiome data. This is the input object that the function processes.

mock_genera

A vector of genera representing the taxa that make up the mock community. These taxa are used to identify mock features to be removed from the phyloseq object.

mock

A logical value determining whether to filter out mock features.

  • TRUE: Remove mock features from the phyloseq object and retain only samples for downstream analysis.

  • FALSE: Retain mock features. Use this option if no mock community is present in the dataset.

Value

A filtered phyloseq object is returned and saved as an RDS file named project_name_phyloseq_asv_level_without_mock.rds in the output_data/rds_files/Before_cleaning_rds_files/ directory.

Details

The function performs the following steps:

  • If mock = FALSE, the function filters the dataset to retain only samples without controls, leaving the mock features intact. This option is suitable for datasets where no mock community is included.

  • If mock = TRUE, the function:

    • Identifies mock features based on the provided mock_genera.

    • Removes the mock features from the dataset.

    • Retains only samples without controls.

Examples

if (FALSE) { # \dontrun{
# Remove mock ASVs from the phyloseq object
physeq_no_mock <- remove_mock(physeq = physeq, mock_genera = c("Mock_Genus1", "Mock_Genus2"), mock = TRUE)

# Retain mock ASVs but filter to only samples (or when no mock community is present)
physeq_no_filter <- remove_mock(physeq = physeq, mock_genera = c("Mock_Genus1", "Mock_Genus2"), mock = FALSE)
} # }