automaticNetworkScreeningGS | R Documentation |
This function performs gene screening based on external gene significance and their network properties.
automaticNetworkScreeningGS(
datExpr, GS,
power = 6, networkType = "unsigned",
detectCutHeight = 0.995, minModuleSize = min(20, ncol(as.matrix(datExpr))/2),
datME = NULL)
datExpr |
data frame containing the expression data, columns corresponding to genes and rows to samples |
GS |
vector containing gene significance for all genes given in |
power |
soft thresholding power used in network construction |
networkType |
character string specifying network type. Allowed values are (unique abbreviations
of) |
detectCutHeight |
cut height of the gene hierarchical clustering dendrogram. See
|
minModuleSize |
minimum module size to be used in module detection procedure. |
datME |
optional specification of module eigengenes. A data frame whose columns are the module eigengenes. If given, module analysis will not be performed. |
Network screening is a method for identifying genes that have a high gene significance and are members
of important modules at the same time.
If datME
is given, the function calls networkScreeningGS
with the default
parameters. If datME
is not given, module eigengenes are first calculated using network analysis
based on supplied parameters.
A list with the following components:
networkScreening |
a data frame containing results of the network screening procedure. See
|
datME |
calculated module eigengenes (or a copy of the input |
hubGeneSignificance |
hub gene significance for all calculated modules. See
|
Steve Horvath
networkScreening
, hubGeneSignificance
,
networkScreening
, cutreeDynamic
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