rifi_penalties: =========================================================================...

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

========================================================================= rifi_penalties

rifi_penalties wraps conveniently all penalty steps

Description

rifi_penalties wraps the functions:

1. make_pen,

2. viz_pen_obj

Usage

rifi_penalties(
  inp,
  details = FALSE,
  viz = FALSE,
  top_i = 25,
  cores = 1,
  dpt = 1,
  smpl_min = 10,
  smpl_max = 100,
  sta_pen = 0.5,
  end_pen = 4.5,
  rez_pen = 9,
  sta_pen_out = 0.5,
  end_pen_out = 4.5,
  rez_pen_out = 9
)

Arguments

inp	SummarizedExperiment: the input data frame with correct format.
details	logical: whether to return the penalty objects or just the logbook.
viz	logical: whether to visualize the output or not. Default is FALSE
top_i	integer: the number of top results visualized. Default is all.
cores	integer: the number of assigned cores for the task.
dpt	integer: the number of times a full iteration cycle is repeated with a more narrow range based on the previous cycle. Default is 2.
smpl_min	integer: the smaller end of the sampling size. Default is 10.
smpl_max	integer: the larger end of the sampling size. Default is 100.
sta_pen	numeric: the lower starting penalty. Default is 0.5.
end_pen	numeric: the higher starting penalty. Default is 4.5.
rez_pen	numeric: the number of penalties iterated within the penalty range. Default is 9.
sta_pen_out	numeric: the lower starting outlier penalty. Default is 0.5.
end_pen_out	numeric: the higher starting outlier penalty. Default is 3.5.
rez_pen_out	numeric: the number of outlier penalties iterated within the outlier penalty range. Default is 7.

Value

The SummarizedExperiment object: with the penalties in the logbook added to the metadata. Also adds logbook_details if details is TRUE, and plots the penalties if viz is TRUE.

See Also

make_pen

viz_pen_obj

Examples

data(fit_minimal)
rifi_penalties(
  inp = fit_minimal, details = FALSE, viz = FALSE,
  top_i = 25, cores = 2, dpt = 1, smpl_min = 10, smpl_max = 100,
  sta_pen = 0.5, end_pen = 4.5, rez_pen = 9, sta_pen_out = 0.5,
  end_pen_out = 4.5, rez_pen_out = 9
)

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