load_bwa_assignment     Efficiently loads a EDGE-produced BWA taxonomic
                        assignment from a file. An assumption has been
                        made - since bwa/EDGE tables are generated in
                        an automated fashion, they should be properly
                        formatted - thus the code doesn't check for any
                        inconsistencies except for the very file
                        existence. Note however, the unassigned to taxa
                        entries are removed. This implementation fully
                        relies on the read.table function from
                        data.table package gaining performance over
                        traditional R techniques.
load_bwa_assignments    Efficiently loads a BWA (or other EDGE-like
                        taxonomic assignment) tables from a list of
                        files. Outputs a named list of assignments.
load_gottcha2_assignment
                        Efficiently loads a GOTTCHA2 (or other
                        EDGE-like taxonomic assignment) table from a
                        file. An assumption has been made - since
                        GOTTCHA2/EDGE tables are generated in an
                        automated fashion, they should be properly
                        formatted - thus the code doesn't check for any
                        inconsistencies except for the very file
                        existence. This implementation fully relies on
                        the read.table function from data.table package
                        gaining performance over traditional R
                        techniques.
load_gottcha2_assignments
                        Efficiently loads a GOTTCHA2 (or other
                        EDGE-like taxonomic assignment) tables from a
                        list of files. Outputs a named list of
                        assignments.
load_gottcha_assignment
                        Efficiently loads a GOTTCHA (or other EDGE-like
                        taxonomic assignment) table from a file. An
                        assumption has been made - since GOTTCHA/EDGE
                        tables are generated in an automated fashion,
                        they should be properly formatted - thus the
                        code doesn't check for any inconsistencies
                        except for the very file existence. This
                        implementation fully relies on the read.table
                        function from data.table package gaining
                        performance over traditional R techniques.
load_gottcha_assignments
                        Efficiently loads a GOTTCHA (or other EDGE-like
                        taxonomic assignment) tables from a list of
                        files. Outputs a named list of assignments.
load_kraken_assignment
                        Efficiently loads a EDGE-produced Kraken
                        taxonomic assignment from a file. An assumption
                        has been made - since Kraken/EDGE tables are
                        generated in an automated fashion, they should
                        be properly formatted - thus the code doesn't
                        check for any inconsistencies except for the
                        very file existence. Note however, the
                        unassigned to taxa entries are removed. This
                        implementation fully relies on the read.table
                        function from data.table package gaining
                        performance over traditional R techniques.
load_kraken_assignments
                        Efficiently loads a GOTTCHA (or other EDGE-like
                        taxonomic assignment) tables from a list of
                        files. Outputs a named list of assignments.
load_metaphlan_assignment
                        Efficiently loads a EDGE-produced Mataphlan
                        taxonomic assignment from a file. An assumption
                        has been made - since Metaphlan/EDGE tables are
                        generated in an automated fashion, they should
                        be properly formatted - thus the code doesn't
                        check for any inconsistencies except for the
                        very file existence. Note however, the
                        unassigned to taxa entries are removed. This
                        implementation fully relies on the read.table
                        function from data.table package gaining
                        performance over traditional R techniques.
load_metaphlan_assignments
                        Efficiently loads a METAPHLAN (or other
                        EDGE-like taxonomic assignment) tables from a
                        list of files. Outputs a named list of
                        assignments.
merge_bwa_assignments   Merges two or more BWA-like taxonomical
                        assignments. The input data frames are assumed
                        to have the following columns: LEVEL, TAXA, and
                        ABUNDANCE - these will be used in the merge
                        procedure, all other columns will be ignored.
merge_bwa_counts        Merges two or more BWA-like taxonomical
                        assignments. The input data frames are assumed
                        to have the following columns: LEVEL, TAXA, and
                        COUNT - these will be used in the merge
                        procedure, all other columns will be ignored.
merge_gottcha_assignments
                        Merges two or more GOTTCHA-like taxonomical
                        assignments. The input data frames are assumed
                        to have the following columns: LEVEL, TAXA, and
                        ABUNDANCE - these will be used in the merge
                        procedure, all other columns will be ignored.
merge_gottcha_counts    Merges two or more GOTTCHA-like taxonomical
                        assignments. The input data frames are assumed
                        to have the following columns: LEVEL, TAXA, and
                        COUNT - these will be used in the merge
                        procedure, all other columns will be ignored.
merge_kraken_assignments
                        Merges two or more Kraken-like taxonomical
                        assignments. The input data frames are assumed
                        to have the following columns: LEVEL, TAXA, and
                        ABUNDANCE - these will be used in the merge
                        procedure, all other columns will be ignored.
merge_metaphlan_assignments
                        Merges two or more Metaphlan-like taxonomical
                        assignments. The input data frames are assumed
                        to have the following columns: LEVEL, TAXA, and
                        ROLLUP - these will be used in the merge
                        procedure, all other columns will be ignored.
plot_bwa_assignment     Generates a single column ggplot for a
                        taxonomic assignment table and also outputs a
                        PDF.
plot_gottcha_assignment
                        Generates a single column ggplot for a
                        taxonomic assignment table and also outputs a
                        PDF.
plot_kraken_assignment
                        Generates a single column ggplot for a
                        taxonomic assignment table and also outputs a
                        PDF.
plot_merged_assignment
                        Generates a single column ggplot for a
                        taxonomic assignment table.
plot_metaphlan_assignment
                        Generates a single column ggplot for a
                        taxonomic assignment table and also outputs a
                        PDF.
