Author: Zhi Huang
lmQCM( data_in, gamma = 0.55, t = 1, lambda = 1, beta = 0.4, minClusterSize = 10, CCmethod = "pearson", normalization = F )
real-valued expression matrix with rownames indicating gene ID or gene symbol
gamma value (default = 0.55)
t value (default = 1)
lambda value (default = 1)
beta value (default = 0.4)
minimum length of cluster to retain (default = 10)
Methods for correlation coefficient calculation (default = "pearson"). Users can also pick "spearman".
Determine if normalization is needed on massive correlation coefficient matrix.
QCMObject - An S4 Class with lmQCM results
# NOT RUN { library(lmQCM) library(Biobase) data(sample.ExpressionSet) data = assayData(sample.ExpressionSet)$exprs data = fastFilter(data, 0.2, 0.2) lmQCM(data) # }
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