Description Usage Arguments Details Value Author(s) Examples
Generate correction and adjacency matrices for data and permutation
1 2 3 | GeneNet(data, labels, caseName, controlName, meanFilter = 0.2,
SDFilter = 0.2, edgeCutoff = 0.004, permutationTimes = 10,
CPUNumbers = 1, folder = "MetaDCN", pathwayDatabase, silent = FALSE)
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data |
a list of matrices (studies) with rows as features and columns as samples. |
labels |
a list of vectors to specify the case/control labels for each subject corresponidng to the columns in each data matrix. |
caseName |
a character string denoting case label. |
controlName |
a character string denoting control label. |
meanFilter |
a number between 0 and 1. Features with mean below this cutoff will be filtered out. |
SDFilter |
a number between 0 and 1. Features with standard deviation (SD) will be filtered out. |
edgeCutoff |
a number between 0 and 1, denoting the proportion of edges to kept. |
permutationTimes |
a number to specify how many permutations to be used. Large number of permutations will be very time-consuming. |
CPUNumbers |
a number to specify how many CPUs are used for parallel, if multicores exists. Must be less than or equal to the permutationTimes. |
folder |
folder path to store results. |
pathwayDatabase |
a list with each element as a vector of pathway genes, and names as pathway names. |
silent |
TRUE/FALSE to specify if suppress screen output. |
This function will generate correction and adjacency matrices for data and permutations.
GeneNet returns a list of information which will be used for SearchBM and MetaDCN function, and several RData files stored in folder path.
List of basic informations for SearchBM and MetaDCN input:
caseName |
case names |
controlName |
control names |
permutationTimes |
permutation times |
folder |
folder path |
pathwayDatabase |
a list of pathways |
CPUNumbers |
CPU numbers from arguments |
AdjacencyMatrices.RData is a list of adjacency matrices for case and control in each study in the order of case studies and control studies.
CorrelationMatrices.RData is a list of correlation matrices for case and control in each study.
AdjacencyMatricesPermutationP.RData is a list of correlation matrices for case and control in each study in permutation P.
Li Zhu (liz86@pitt.edu)
1 2 3 4 5 | data(pathwayDatabase)
data(example)
GeneNetRes <- GeneNet(data_2l, labels_2l, caseName="inv(16)", controlName="t(8;21)", meanFilter=0.8, SDFilter=0.8, edgeCutoff=0.1, permutationTimes=4, CPUNumbers=1, folder="MetaDCN", pathwayDatabase, silent=FALSE)
SearchBMRes <- SearchBM(GeneNetRes, MCSteps=500, jaccardCutoff=0.8, repeatTimes=3, outputFigure=TRUE, silent=FALSE)
MetaDNCRes <- MetaDCN(GeneNetRes, SearchBMRes, FDRCutoff=0.3, w1=NULL, silent=FALSE)
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