fold_change: =========================================================================...

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

========================================================================= fold_change

fold_change sets a fold-change ratio between the neighboring fragments of Half-life (HL) and intensity

Description

fold_change sets fold change on intensity and fold change HL fragments of two successive fragments. Two intensity fragments could belong to one HL fragment. This function sets first the borders using the position and applies the fold change ratio between the neighboring fragments of HL and those from intensity log2(intensity frgA/intensity frgB/half-life frgA/half-life frgB). All grepped fragments are from the same TU excluding outliers.

Usage

fold_change(inp)

Arguments

inp	SummarizedExperiment: the input data frame with correct format.

Details

The function used is: synthesis_r_Function: assigns events depending on the ratio between HL and intensity of two consecutive fragments. intensity(int) = synthesis rate(k)/decay(deg) (steady state), int1/int2 = k1/deg1*deg2/k2 int1 * (deg1/int2) * deg2 = k1/k2 => synthesis ratio. In case of synthesis ratio is: synthesis ratio > 0 -> New start synthesis ratio < 0 -> Termination

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.

p_value_slope:

Integer, the p_value added to the inp.

delay_frg_slope:

Integer, the slope value of the fit through the respective delay fragment.

velocity_ratio:

Integer, the ratio value of velocity from 2 delay fragments.

event_position:

Integer, position of the event added to the input.

FC_HL:

Integer, the fold change value of 2 HL fragments.

FC_fragment_HL:

String, the fragments corresponding to HL fold change.

p_value_HL:

Integer, the p_value added to the input of 2 HL fragments.

FC_intensity:

Integer, the fold change value of 2 intensity fragments.

FC_fragment_intensity:

String, the fragments corresponding to intensity fold change.

p_value_intensity:

Integer, the p_value added to the input of 2 intensity fragments.

synthesis_ratio:

Integer, the value correspomding to synthesis rate.

synthesis_ratio_event:

String, the event assigned by synthesis rate either Termination or iTSS.

FC_HL_intensity:

Integer, the value corresponding to HL and intensity fold change.

FC_HL_intensity_fragment:

String, the fragments corresponding to intensity and HL fold change.

FC_HL_adapted:

Integer, the fold change of half-life/ fold change of intensity,position of the half-life fragment is adapted to intensity fragment.

Examples

data(stats_minimal)
fold_change(inp = stats_minimal)

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