rifi_stats: rifi_stats wraps all statistical prediction steps...

In CyanolabFreiburg/rifi: 'rifi' analyses data from rifampicin time series created by microarray or RNAseq

rifi_stats wraps all statistical prediction steps conveniently

Description

rifi_stats wraps the functions:

1. predict_ps_itss

2. apply_Ttest_delay

3. apply_ancova

4. apply_event_position

5. apply_t_test

6. fold_change

7. apply_manova

8. apply_t_test_ti

9. gff3_preprocess

Usage

rifi_stats(inp, dista = 300, path)

Arguments

inp	SummarizedExperiment: the input data frame with correct format.
dista	integer: the maximal distance allowed between two successive fragments. Default is the auto generated value.
path	path: to the directory containing the gff3 file.

Value

The SummarizedExperiment object: ID with position, strand, intensity, probe_TI, flag, position_segment, delay, half_life, TI_termination_factor, delay_fragment, velocity_fragment, intercept, slope, HL_fragment, HL_mean_fragment, intensity_fragment, intensity_mean_fragment, TU, TI_termination_fragment, TI_mean_termination_factor, seg_ID, pausing_site, iTSS_I, ps_ts_fragment, event_ps_itss_p_value_Ttest, p_value_slope, delay_frg_slope, velocity_ratio, event_duration, event_position, FC_HL, FC_fragment_HL, p_value_HL, FC_intensity, FC_fragment_intensity, p_value_intensity, FC_HL_intensity, FC_HL_intensity_fragment, FC_HL_adapted, synthesis_ratio, synthesis_ratio_event, p_value_Manova, p_value_TI, TI_fragments_p_value

See Also

predict_ps_itss

apply_Ttest_delay

apply_ancova

apply_event_position

apply_t_test

fold_change

apply_manova

apply_t_test_ti

gff3_preprocess

Examples

data(fragmentation_minimal)
rifi_stats(inp = fragmentation_minimal, dista = 300, 
path = gzfile(system.file("extdata", "gff_e_coli.gff3.gz",
package = "rifi")))

CyanolabFreiburg/rifi documentation built on May 7, 2023, 7:53 p.m.