fragment_delay: =========================================================================...

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

========================================================================= fragment_delay

fragment_delay performs the delay fragmentation

Description

fragment_delay makes delay_fragments based on position_segments and assigns all gathered information to the SummarizedExperiment object. The columns "delay_fragment", "velocity_fragment", "intercept" and "slope" are added. fragment_delay makes delay_fragments, assigns slopes, which are 1/velocity at the same time, and intercepts for the TU calculation. The function used is: score_fun_linear the input is the SummarizedExperiment object. pen is the penalty for new fragments in the dynamic programming, pen_out is the outlier penalty.

Usage

fragment_delay(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.

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.

Examples

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

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