# 'rifi' analyses data from rifampicin time series created by microarray or RNAseq

## Documentation for package ‘rifi’ version 1.6.0

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

## Help Pages

apply_ancova | ========================================================================= apply_ancova: apply_ancova checks the variances between 2 segments showing either pausing site (ps) or internal starting site (ITSS) independently.
apply_event_position | ========================================================================= apply_event_position: apply_event_position extracts event time duration for pausing site or iTSS
apply_manova | ========================================================================= apply_manova: apply_manova checks if the ratio of hl ratio and intensity ratio is statistically significant.
apply_Ttest_delay | ========================================================================= apply_Ttest_delay: apply_Ttest_delay checks the significance of the point between 2 segments showing pausing site (ps) and internal starting site (ITSS) independently
apply_t_test | ========================================================================= apply_t_test: apply_t_test uses the statistical t_test to check if the fold-change of half -life (HL) fragments and the fold-change intensity fragments respectively are significant.
apply_t_test_ti | ========================================================================= apply_t_test_ti: apply_t_test_ti compares the mean of two neighboring TI fragments within the same TU.
check_input | ========================================================================= Check_input: Check_input reviews the input given by the user
dataframe_summary | ========================================================================= dataframe_summary: dataframe_summary creates two tables relating gene annotation to fragments
dataframe_summary_events | ========================================================================= dataframe_summary_events: dataframe_summary_events creates one table with all events between the segments
dataframe_summary_events_HL_int | ========================================================================= dataframe_summary_events_HL_int: dataframe_summary_events_HL_int creates one table with all events between the segments
dataframe_summary_events_ps_itss | ========================================================================= dataframe_summary_events_ps_itss: dataframe_summary_events_ps_itss creates one table with all events between the segments.
dataframe_summary_events_velocity | ========================================================================= dataframe_summary_events_velocity: dataframe_summary_events_velocity creates one table with all events between the segments.
dataframe_summary_TI | ========================================================================= dataframe_summary_TI: dataframe_summary_TI creates one table with all TI fragments,p_value and the coordinates
event_dataframe | ========================================================================= event_dataframe: event_dataframe creates a dataframe only with events
example_input_e_coli | An example SummarizedExperiment from E. coli An example SummarizedExperiment from RNA-seq containing information about the intensities at all time points (assay). Seqnames, IRanges and strand columns (rowRanges)and colData with time point series and replicates.
example_input_minimal | An artificial example SummarizedExperiment An example SummarizedExperiment containing information about the intensities at all time points (assay). Seqnames, IRanges and strand columns (rowRanges) and colData with time point series and replicates.
example_input_synechocystis_6803 | An example input data frame from Synechocystis PCC 6803 A SummarizedExperiment from microarrays data containing information about the intensities at all time points (assay), Seqnames, IRanges and strand columns (rowRanges) and colData with time point series and averaged replicates.
finding_PDD | ========================================================================= finding_PDD: finding_PDD Flags potential candidates for post transcription decay
finding_TI | ========================================================================= finding_TI: finding_TI flags potential candidates for transcription interference
fit_e_coli | The result of rifi_fit for E.coli example data A SummarizedExperiment containing the output from rifi_fit as an extension of rowRanges and metadata.
fit_minimal | The artificial result of rifi_fit for artificial example data A SummarizedExperiment containing the output from rifi_fit.
fit_synechocystis_6803 | The result of rifi_fit for Synechocystis 6803 example data A SummarizedExperiment containing the output from rifi_fit as an extension of rowRanges and metadata.
fold_change | ========================================================================= fold_change: fold_change sets a fold-change ratio between the neighboring fragments of Half-life (HL) and intensity
fragmentation_e_coli | The result of rifi_fragmentation for E.coli example data A SummarizedExperiment containing the output from rifi_fragmentation as an extension of rowRanges
fragmentation_minimal | The result of rifi_fragmentation for artificial example data A SummarizedExperiment containing the output from rifi_fragmentation as an extension of rowRanges and metadata.
fragmentation_synechocystis_6803 | The result of rifi_fragmentation for Synechocystis 6803 example data A SummarizedExperiment containing the output from rifi_fragmentation as an extension fo rowRanges
fragment_delay | ========================================================================= fragment_delay: fragment_delay performs the delay fragmentation
fragment_HL | ========================================================================= fragment_HL: fragment_HL performs the half_life fragmentation
fragment_inty | ========================================================================= fragment_inty: fragment_inty performs the intensity fragmentation
fragment_TI | ========================================================================= fragment_TI: fragment_TI performs the TI fragmentation
gff3_preprocess | ========================================================================= gff3_preprocess: gff3_preprocess process gff3 file from database for multiple usage
make_df | ========================================================================= make_df: make_df adds important columns to the SummarizedExperiment object
make_pen | ========================================================================= make_pen: make_pen assigns automatically a penalties
nls2_fit | ========================================================================= nls2_fit: nls2_fit estimates decay for each probe or bin
penalties_e_coli | The result of rifi_penalties for E.coli example data. A SummarizedExperiment containing the output from rifi_penalties including the logbook and the four penalty objects as metadata.
penalties_minimal | The result of rifi_penalties for artificial example data A SummarizedExperiment containing the output from rifi_penalties including the logbook and the four penalty objects as metadata.
penalties_synechocystis_6803 | The result of rifi_penalties for Synechocystis 6803 example data. A SummarizedExperiment containing the output from rifi_penalties including the logbook and the four penalty objects as metadata.
predict_ps_itss | ========================================================================= predict_ps_itss: predict_ps_itss predicts pausing sites (ps) and internal starting sites (ITSS) between delay fragments.
preprocess_e_coli | The result of rifi_preprocess for E.coli example data A SummarizedExperiment containing the output from rifi_penalties including the logbook and the four penalty objects as metadata. A list containing the output from rifi_preprocess, including the inp and the modified input_df.
preprocess_minimal | The result of rifi_preprocess for artificial example data A SummarizedExperiment containing the output from rifi_preprocess
preprocess_synechocystis_6803 | The result of rifi_preprocess for Synechocystis 6803 example data is a A SummarizedExperiment containing the output of rifi_preprocess as an extention to rowRanges
res_minimal | The result of event_dataframe for E.coli artificial example. A data frame combining the processed genome annotation and a SummarizedExperiment data from rifi_stats. The dataframe is
rifi_fit | ========================================================================= rifi_fit: rifi_fit wraps conveniently all fitting steps
rifi_fragmentation | ========================================================================= rifi_fragmentation: rifi_fragmentation wraps conveniently all fragmentation steps
rifi_penalties | ========================================================================= rifi_penalties: rifi_penalties wraps conveniently all penalty steps
rifi_preprocess | ========================================================================= rifi_preprocess: rifi_preprocess wraps conveniently all pre-processing steps
rifi_stats | rifi_stats wraps all statistical prediction steps conveniently
rifi_summary | ========================================================================= rifi_summary: rifi_summary wraps conveniently and summarize all rifi outputs
rifi_visualization | ========================================================================= rifi_visualization: rifi_visualization plots all the data with fragments and events from both strands
rifi_wrapper | ========================================================================= rifi_wrapper: rifi_wrapper wraps conveniently all functions included on rifi workflow
segment_pos | ========================================================================= segment_pos: segment_pos divides all IDs by position into position_segments
stats_e_coli | The result of rifi_stats for E.coli example data A SummarizedExperiment containing the output from rifi_stats
stats_minimal | The result of rifi_stats for artificial example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRanges and metadata (gff file processed, see gff file documentation)
stats_synechocystis_6803 | The result of rifi_stats for Synechocystis 6803 example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRanges
summary_e_coli | The result of rifi_summary for E.coli example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRanges
summary_minimal | The result of rifi_summary for artificial example data A SummarizedExperiment with the output from rifi_summary as metadata
summary_synechocystis_6803 | The result of rifi_summary for Synechocystis 6803 example data A list containing the output from rifi_summary, including the fragment based data frame, bin based data frame, event data frame and the TI dataframe.
TI_fit | ========================================================================= TI_fit: TI_fit estimates transcription interference and termination factor using nls function for probe or bin flagged as "TI".
TUgether | ========================================================================= TUgether: TUgether combines delay fragments into TUs
viz_pen_obj | ========================================================================= viz_pen_obj: viz_pen_obj visualizes penalty objects
wrapper_e_coli | The result of rifi_wrapper for E.coli example data A list of SummarizedExperiment containing the output of rifi_wrapper. The list contains 6 elements of SummarizedExperiment output of rifi_preprocess, rifi_fit, rifi_penalties, rifi_fragmentation, rifi_stats and rifi_summary. The plot is generated from rifi_visualization. for more detail, please refer to each function separately.

wrapper_minimal

The result of rifi_wrapper for E.coli artificial example. A list of SummarizedExperiment containing the output of rifi_wrapper. The list contains 6 elements of SummarizedExperiment output of rifi_preprocess, rifi_fit, rifi_penalties, rifi_fragmentation, rifi_stats and rifi_summary. The plot is generated from rifi_visualization. for more detail, please refer to each function separately.

wrapper_summary_synechocystis_6803

The result of rifi_wrapper for summary_synechocystis_6803 example data A list of SummarizedExperiment containing the output of rifi_wrapper. The list contains 6 elements of SummarizedExperiment output of rifi_preprocess, rifi_fit, rifi_penalties, rifi_fragmentation, rifi_stats and rifi_summary. The plot is generated from rifi_visualization. for more detail, please refer to each function separately.