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

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Documentation for package ‘rifiComparative’ version 1.9.0

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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