makeCNOlist: Make a CNOlist structure

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/makeCNOlist.R

Description

This function takes as input the output of readMIDAS and extracts the elements that are needed in a CNO project. Instead, please use the CNOlist class to read a MIDAS file that will be converted to a CNOlist.

Usage

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makeCNOlist(dataset, subfield, verbose=TRUE)

Arguments

dataset

output of readMIDAS

subfield

TRUE or FALSE, specifies if the column headers contain subfields or not i.e. if I should look for TR:sthg:sthg or just TR:sthg.

verbose

logical (default to TRUE) print information on the screen.

Details

Be aware that most of the functions in this package, including this one, expect the data to contain measurements at time 0, but these should all be equal to zero according to the normalisation procedure that should be used. Therefore, if you have one time point, the files valueSignals contains two matrices, one for t0 and one for t1.

If there are replicate rows in the MIDAS file (i.e., identical cues and identical time), this function averages the values of the measurements for these replicates.

Columns with the following tags are ignored: NOINHIB, NO-INHIB, NO-LIG, NOCYTO.

Value

a CNOlist with fields

namesCues

a vector of names of cues

namesStimuli

a vector of names of stimuli

namesInhibitors

a vector of names of inhibitors

namesSignals

a vector of names of signals

timeSignals

a vector of times

valueCues

a matrix of dimensions nConditions x nCues, with 0 or 1 if the cue is present or absent in the particular condition

valueInhibitors

a matrix of dimensions nConditions x nInhibitors, with 0 or 1 if the inhibitor is present or absent in the particular condition

valueStimuli

of dimensions nConditions x nStimuli, with 0 or 1 if the stimuli is present or absent in the particular condition

valueSignals

a list of the same length as timeSignals, each element containing a matrix of dimensions nConditions x nsignals, with the measurements.

valueVariances

a list of the same length as timeSignals, each element containing a matrix of dimensions nConditions x nsignals, with the standard deviation of the replicates.

Author(s)

C. Terfve, T. Cokelaer

References

J. Saez-Rodriguez, L. G. Alexopoulos, J. Epperlein, R. Samaga, D. A. Lauffenburger, S. Klamt and P. K. Sorger. Discrete logic modeling as a means to link protein signaling networks with functional analysis of mammalian signal transduction, Molecular Systems Biology, 5:331, 2009.

See Also

readMIDAS, CNOlist-class

Examples

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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)

Example output

Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package:BiocGenericsThe following objects are masked frompackage:parallel:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked frompackage:stats:

    IQR, mad, sd, var, xtabs

The following objects are masked frompackage:base:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: hash
hash-2.2.6.1 provided by Decision Patterns

Loading required package: RCurl
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML

Attaching package:XMLThe following object is masked frompackage:graph:

    addNode

Loading required package: ggplot2
[1] TRUE TRUE TRUE
[1] "Your data set comprises  18 conditions (i.e. combinations of time point and treatment)"
[1] "Your data set comprises measurements on  7  different species"
[1] "Your data set comprises  4 stimuli/inhibitors and 1 cell line(s) ( mock )"
[1] "Please be aware that CNO only handles measurements on one cell line at this time."
[1] "Your data file contained 'NaN'. We have assumed that these were missing values and replaced them by NAs."
[1] "Please be aware that if you only have some conditions at time zero (e.g.only inhibitor/no inhibitor), the measurements for these conditions will be copied across matching conditions at t=0"

CellNOptR documentation built on Nov. 8, 2020, 6:58 p.m.