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. |