apply_Ttest_delay: =========================================================================...

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

========================================================================= 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

Description

apply_Ttest_delay: is a statistical test to check the significance of the point between 2 segments showing pausing site (ps) and internal starting site (ITSS) independently. The function uses t-test. The last point from the first segment and the first point from the second segment are selected and added to the residuals of each model. The sum is subjected to t-test.

Usage

apply_Ttest_delay(inp)

Arguments

inp	SummarizedExperiment: the input data frame with correct format.

Value

the SummarizedExperiment with the columns regarding statistics:

ID:

The bin/probe specific ID.

position:

The bin/probe specific position.

strand:

The bin/probe specific strand.

intensity:

The relative intensity at time point 0.

probe_TI:

An internal value to determine which fitting model is applied.

flag:

Information on which fitting model is applied.

position_segment:

The position based segment.

delay:

The delay value of the bin/probe.

half_life:

The half-life of the bin/probe.

TI_termination_factor:

String, the factor of TI fragment.

delay_fragment:

The delay fragment the bin belongs to.

velocity_fragment:

The velocity value of the respective delay fragment.

intercept:

The vintercept of fit through the respective delay fragment.

slope:

The slope of the fit through the respective delay fragment.

HL_fragment:

The half-life fragment the bin belongs to.

HL_mean_fragment:

The mean half-life value of the respective half-life fragment.

intensity_fragment:

The intensity fragment the bin belongs to.

intensity_mean_fragment:

The mean intensity value of the respective intensity fragment.

TU:

The overarching transcription unit.

TI_termination_fragment:

The TI fragment the bin belongs to.

TI_mean_termination_factor:

The mean termination factor of the respective TI fragment.

seg_ID:

The combined ID of the fragment.

pausing_site:

presence of pausing site indicated by +/-.

iTSS_I:

presence of iTSS_I indicated by +/-.

ps_ts_fragment:

The fragments involved in pausing site or iTSS_I.

event_duration:

Integer, the duration between two delay fragments.

event_ps_itss_p_value_Ttest:

p_value of pausing site or iTSS_I.

Examples

data(stats_minimal)
apply_Ttest_delay(inp = stats_minimal)

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