buildInputs: Function to generate the data inputs of PHONEMeS

In saezlab/PHONEMeS-ILP: Building logic-based models from discovery high-content phosphoproteomics data

Function to generate the data inputs of PHONEMeS

Description

Building the PHONEMeS inputs from the differential analysis results obtained from the Limma analysis

Arguments

tableTopList	a list of table-top contiaing the differential analysis results obtained from Limma. Tables for each comparison/experiment should be combined in one list.
fcThresh	a numberc value or a vector of values (for each experimental condition) indicating the threshold of significance (as a log2) (sites with regulation levels higher than the set significance are considered as perturbed. default set to NULL)
pThresh	a p-value threshold parameter (or vector if different threshold should be applied for different comparisons) to indicate which sites/measurements are considered as significant
idxID	the index indicating which column of the table-top contains the sites identifiers (default: 1)
idxFC	the index indicating which column of the table-top contains the FC values (default: 2)
idxPval	the index indicating which column of the table-top contains the p-values (default: 6, the adjusted p-values column of the table-tops returned by Limma)
mappingTable	if user wishes to plot on the solution identifiers different than what is on the measurements table then he should provide a mapping table (default: NULL)
namesConditions	a vector of experimental conditions to name each experiment in hte output
directionality	a string character indicating whether the directionality of the measurement should be considered for a site to be consiidered as perturbed. It can take three values: up - measurements with log2FC which are positive and higher than fcThresh are considered as perturbed; down - measurements with log2FC which are negative and lower than fcThresh are considered as perturbed; no - measurement whose absolute log2FC value is higher than fcThresh are considered as perturbed. Default: no.

Value

This function returns the data inputs used for the PHONEMeS analysis.

Author(s)

E. Gjerga

saezlab/PHONEMeS-ILP documentation built on June 21, 2022, 5:36 p.m.