rifi_fragmentation: =========================================================================...

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

========================================================================= rifi_fragmentation

rifi_fragmentation wraps conveniently all fragmentation steps

Description

rifi_fragmentation is wrapper of the following functions:

1. fragment_delay

2. fragment_HL

3. fragment_inty

4. TUgether

5. fragment_TI

Usage

rifi_fragmentation(
  inp,
  cores = 1,
  pen_delay = NULL,
  pen_out_delay = NULL,
  pen_HL = NULL,
  pen_out_HL = NULL,
  pen_inty = NULL,
  pen_out_inty = NULL,
  pen_TU = NULL,
  pen_TI = NULL,
  pen_out_TI = NULL
)

Arguments

inp	SummarizedExperiment: the input data frame with correct format.
cores	integer: the number of assigned cores for the task.
pen_delay	numeric: an internal parameter for the dynamic programming. Higher values result in fewer fragments. Default is the auto generated value.
pen_out_delay	numeric: an internal parameter for the dynamic programming. Higher values result in fewer allowed outliers. Default is the auto generated value.
pen_HL	numeric: an internal parameter for the dynamic programming. Higher values result in fewer fragments. Default is the auto generated value.
pen_out_HL	numeric: an internal parameter for the dynamic programming. Higher values result in fewer allowed outliers. Default is the auto generated value.
pen_inty	numeric: an internal parameter for the dynamic programming. Higher values result in fewer fragments. Default is the auto generated value.
pen_out_inty	numeric: an internal parameter for the dynamic programming. Higher values result in fewer allowed outliers. Default is the auto generated value.
pen_TU	numeric: an internal parameter for the dynamic programming. Higher values result in fewer fragments. Default -0.75.
pen_TI	numeric: an internal parameter for the dynamic programming. Higher values result in fewer fragments. Default is the auto generated value.
pen_out_TI	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: with delay_fragment, HL_fragment, intensity_fragment, TI_termination_fragment and TU, and the respective values added to the rowRanges.

See Also

fragment_delay

fragment_HL

fragment_inty

TUgether

fragment_TI

Examples

data(penalties_minimal)
rifi_fragmentation(inp = penalties_minimal, cores = 2)

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