# 'rifiComparative' compares the output of rifi from two different conditions.

## Documentation for package ‘rifiComparative’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
fragmentation | fragmentation: Conveniently wraps all fragmentation steps
fragment_int | The result of fragmentation for df_comb_minimal example data A data frame containing the output of fragmentation as a data frame
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
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
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.
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