adjusting_HLToInt       adjusting_HLToInt Creates one table merging HL
                        and intensity fragments with genome annotation
annot_g                 The result of gff3_preprocessing of gff3 file A
                        list containing all necessary information from
                        a gff file for adjusting_HLToInt and
                        visualization.
data_combined_minimal   The result of joining_by_row for inp_s and
                        inp_f example data A data frame containing the
                        output of joining_by_row as a data frame
df_comb_minimal         The result of joining_by_column for
                        data_combined_minimal example data A data frame
                        containing the output of joining_by_row as a
                        data frame
df_mean_minimal         The result of adjusting_HLToInt for
                        stats_df_comb_minimal and annotation example
                        data A data frame containing the output of
                        adjusting_HLToInt as a data frame
differential_expression
                        An example data frame from Synechosystis PCC
                        6803 differential probes expression obtained
                        from limma package and only interesting
                        variables were selected. The data frame was
                        used entirely.
figures_fun             'figures_fun': generates several plots
fragment_int            The result of fragmentation for df_comb_minimal
                        example data A data frame containing the output
                        of fragmentation as a data frame
fragmentation           fragmentation: Conveniently wraps all
                        fragmentation steps
gff3_preprocess         gff3_preprocess processes gff3 file from
                        database
inp_f                   The result of loading_fun for stats_se_cdt2
                        example data Two data frame containing the
                        output of loading_fun as second element of a
                        list.
inp_s                   The result of loading_fun for stats_se_cdt1
                        example data Two data frame containing the
                        output of loading_fun as first element of a
                        list.
joining_data_column     joining_data_column joins two data frames by
                        column
joining_data_row        joining_data_row joins two data frames by row
loading_fun             loading_fun loads the data of all conditions
make_pen                make_pen assigns automatically penalties
pen_HL                  The result of penalties for df_comb_minimal
                        example data. A list containing the output from
                        penalties including the logbook and two penalty
                        objects.
pen_int                 The result of penalties for df_comb_minimal
                        example data. A list containing the output from
                        penalties including the logbook and two penalty
                        objects.
penalties               penalties wraps conveniently all penalty steps
penalties_df            The result of penalties for df_comb_minimal
                        example data A data frame containing the output
                        of penalties as a data frame
rifiComparative         =============================================================================
                        rifiComparative: rifiComparative a successor
                        package of rifi. It compares 2 rifi outputs
                        from 2 different conditions of the same
                        organism.
rifi_visualization_comparison
                        rifi_visualization_comparison plots the
                        segments and genome annotation
statistics              statistics check segments significance using
                        statistical test
stats_df_comb_minimal   The result of statistics for fragment_int
                        example data A data frame containing the output
                        of statistics as a data frame
stats_se_cdt1           An example SummarizedExperiment from
                        Synechosystis PCC 6803 first condition obtained
                        from rifi_statistics and used as input for
                        rifiComparative
stats_se_cdt2           An example SummarizedExperiment from
                        Synechosystis PCC 6803 second condition
                        obtained from rifi_statistics and used as input
                        for rifiComparative
