rifi_fit: =========================================================================...

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

========================================================================= rifi_fit

rifi_fit wraps conveniently all fitting steps

Description

rifi_fit wraps the functions:

1. nls2_fit

2. TI_fit

3. plot_nls2_function

4. plot_singleProbe_function

Usage

rifi_fit(
  inp,
  cores = 1,
  viz = FALSE,
  restr = 0.2,
  decay = seq(0.08, 0.11, by = 0.02),
  delay = seq(0, 10, by = 0.1),
  k = seq(0.1, 1, 0.2),
  bg = 0.2,
  TI_k = seq(0, 1, by = 0.5),
  TI_decay = c(0.05, 0.1, 0.2, 0.5, 0.6),
  TI = seq(0, 1, by = 0.5),
  TI_delay = seq(0, 2, by = 0.5),
  TI_rest_delay = seq(0, 2, by = 0.5),
  TI_bg = 0
)

Arguments

inp	SummarizedExperiment: the input with correct format.
cores	integer: the number of assigned cores for the task.
viz	logical: whether to visualize the output.
restr	numeric: a parameter that restricts the freedom of the fit to avoid wrong TI-term_factors, ranges from 0 to 0.2
decay	numeric vector: A sequence of starting values for the decay. Default is seq(.08, 0.11, by=.02)
delay	numeric vector: A sequence of starting values for the delay. Default is seq(0,10, by=.1)
k	numeric vector: A sequence of starting values for the synthesis rate.Default is seq(0.1,1,0.2)
bg	numeric vector: A sequence of starting values. Default is 0.2.
TI_k	numeric vector: A sequence of starting values for the synthesis rate. Default is seq(0, 1, by = 0.5).
TI_decay	numeric vector: A sequence of starting values for the decay. Default is c(0.05, 0.1, 0.2, 0.5, 0.6).
TI	numeric vector: A sequence of starting values for the TI. Default is seq(0, 1, by = 0.5).
TI_delay	numeric vector: A sequence of starting values for the delay. Default is seq(0, 2, by = 0.5).
TI_rest_delay	numeric vector: A sequence of starting values. Default is seq(0, 2, by = 0.5).
TI_bg	numeric vector: A sequence of starting values. Default is 0.

Value

the SummarizedExperiment object: with delay, decay and TI_termination_factor added to the rowRanges. The full fit data is saved in the metadata as "fit_STD" and "fit_TI". A plot is given if viz = TRUE.

See Also

nls2_fit

TI_fit

plot_nls2

plot_singleProbe

Examples

data(preprocess_minimal)
rifi_fit(
  inp = preprocess_minimal,
  cores = 1, viz = FALSE, restr = 0.1,
  decay = seq(.08, 0.11, by = .02),
  delay = seq(0, 10, by = .1), k = seq(0.1, 1, 0.2), bg = 0.2,
  TI_k = seq(0, 1, by = 0.5), TI_decay = c(0.05, 0.1, 0.2, 0.5, 0.6),
  TI = seq(0, 1, by = 0.5), TI_delay = seq(0, 2, by = 0.5),
  TI_rest_delay = seq(0, 2, by = 0.5), TI_bg = 0
)

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