rifi_wrapper: =========================================================================...

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

========================================================================= rifi_wrapper

rifi_wrapper wraps conveniently all functions included on rifi workflow

Description

rifi_wrapper wraps the functions:

1. rifi_preprocess

2. rifi_fit

3. rifi_penalties

4. rifi_fragmentation

5. rifi_stats

6. rifi_summary

7. rifi_visualization.

Usage

rifi_wrapper(inp, cores, path, bg, restr)

Arguments

inp	data frame: the input data frame with correct format.
cores	integer: the number of assigned cores for the task.
path	path: path to an annotation file in gff format.
bg	numeric: threshold over which the last time point has to be to be fitted with the above background mode.
restr	numeric: a parameter that restricts the freedom of the fit to avoid wrong TI-term_factors, ranges from 0 to 0.2

Value

All intermediate objects

See Also

rifi_preprocess

rifi_fit

rifi_penalties

rifi_fragmentation

rifi_stats

rifi_summary

rifi_visualization

Examples

data(example_input_minimal)
rifi_wrapper(inp = example_input_minimal, cores = 2, path = 
gzfile(system.file("extdata", "gff_e_coli.gff3.gz", package = "rifi")), 
bg = 0, restr = 0.01)

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