fragment_TI: =========================================================================...

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

========================================================================= fragment_TI

fragment_TI performs the TI fragmentation

Description

fragment_TI makes TI_fragments based on TUs and assigns all gathered information to the SummarizedExperiment object. The columns TI_termination_fragment" and the TI_mean_termination_factor are added.

Usage

fragment_TI(inp, cores = 1, pen, pen_out)

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 is the auto generated value.
pen_out	numeric: an internal parameter for the dynamic programming. Higher values result in fewer allowed outliers. Default is the auto generated value.

Details

The function used is:

.score_fun_ave.

The input is the SummarizedExperiment object.

pen is the penalty for new fragments in the dynamic programming, pen_out is the outlier penalty.

Value

The SummarizedExperiment object:

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
TI_termination_fragment:	The TI fragment the bin belongs to
TI_mean_termination_factor:	The mean termination factor of the respective TI fragment

Examples

data(fragmentation_minimal)
fragment_TI(inp = fragmentation_minimal, cores = 2, pen = 2, pen_out = 1)

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