TUgether: =========================================================================...

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

========================================================================= TUgether

TUgether combines delay fragments into TUs

Description

TUgether combines delay fragments into TUs. The column "TU" is added. It uses score fun_increasing on the start and end points of delay_fragments.

Usage

TUgether(inp, cores = 1, pen = -0.75)

Arguments

inp	SummarizedExperiment: the input data frame with correct format.
cores	cores: integer: the number of assigned cores for the task.
pen	numeric: an internal parameter for the dynamic programming. Higher values result in fewer fragments. Default -0.75.

Details

The function used is: .score_fun_increasing

The input is the SummarizedExperiment object. pen is the penalty for new fragments in the dynamic programming. Since high scores are aimed, pen is negative.

Value

The SummarizedExperiment with the columns regarding the TU:

ID:

The bin/probe specific ID.

position:

The bin/probe specific position.

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.

Examples

data(fragmentation_minimal)
TUgether(inp = fragmentation_minimal, cores = 2, pen = -0.75)

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