finding_TI: =========================================================================...

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

========================================================================= finding_TI

finding_TI flags potential candidates for transcription interference

Description

finding_TI uses 'score_fun_ave' to make groups by the mean of "probe_TI". "TI" is added to the "flag" column. TI is characterized by relative intensities at time points later than "0". The rowRanges need to contain at least "ID", "probe_TI" and "position_segment"!

Usage

finding_TI(inp, cores, pen = 10, thrsh = 0.5, add = 1000)

Arguments

inp	SummarizedExperiment: the input.
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. Advised to be kept at 10. Default is 10.
thrsh	numeric: an internal parameter that allows fragments with a certain amount of IDs with higher relative intensities at time points later than "0" to be flagged as "TI". Higher values result in fewer candidates. -0.5 is 25 %, 0 is 50%, 0.5 is 75%. Advised to be kept at 0.5. Default is 0.5.
add	integer: range of nucleotides before and after a potential TI event wherein IDs are fitted with the TI fit.

Value

The SummarizedExperiment object: with "TI" added to the flag column.

Examples

data(preprocess_minimal)
finding_TI(inp = preprocess_minimal, cores = 2, pen = 10, thrsh = 0.5,
add = 1000)

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