readMIDAS: Reads in a CSV MIDAS file

In cokelaer/CellNOptR: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Description

This function takes in a single argument, the name of a CSV MIDAS file containing the data, and returns a list that contains all the elements to build a CNOlist. The output of this function should be used as input for makeCNOlist.

Usage

readMIDAS(MIDASfile, verbose=TRUE)

Arguments

MIDASfile	a CSV MIDAS file (see details)
verbose	logical (default to TRUE).

Details

This function does not return a CNOlist, but the output of this function can be used directly into makeCNOlist to create one. The MIDAS file format is described in Saez-Rodriguez et al. (2008).

If you have all of the readouts measured at the same series of time points, you can specify a unique DA: column which must have the format "DA:ALL".

Value

this function returns a list with fields:

dataMatrix	matrix containing the data in the MIDAS file
TRcol	indexes of the columns that contain the treatments (excluding cell line)
DAcol	indexes of the columns that contain the data time points
DVcol	indexes of the columns that contain the actual values (measurements)

Author(s)

C.Terfve

References

J. Saez-Rodriguez, A. Goldsipe, J. Muhlich, L. Alexopoulos, B. Millard, D. A. Lauffenburger, P. K. Sorger Flexible Informatics for Linking Experimental Data to Mathematical Models via DataRail. Bioinformatics, 24:6, 840-847 (2008).

See Also

makeCNOlist

Examples

   tmpdir<-tempdir()
   setwd(tmpdir)
   cpfile<-dir(system.file("ToyModel",package="CellNOptR"),full=TRUE)
   file.copy(from=cpfile,to=getwd(),overwrite=TRUE)
   dataToy<-readMIDAS(MIDASfile='ToyDataMMB.csv')
   CNOlistToy<-makeCNOlist(dataset=dataToy,subfield=FALSE)

cokelaer/CellNOptR documentation built on May 27, 2019, 8:44 a.m.