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 |