Usage
vectorTOM(
datExpr,
vect,
subtract1 = FALSE,
blockSize = 2000,
corFnc = "cor", corOptions = "use = 'p'",
networkType = "unsigned",
power = 6,
verbose = 1, indent = 0)
Arguments
datExpr
a data frame containing the expression data of the whole set,
with rows corresponding to samples and columns to genes.
vect
a single vector or a matrix-like object containing vectors whose topological overlap is to
be calculated.
subtract1
logical: should calculation be corrected for self-correlation? Set this to
TRUE if vect contains a subset of datExpr.
blockSize
maximum block size for correlation calculations. Only important if vect
contains a large number of columns.
corFnc
character string giving the correlation function to be used for the adjacency
calculation. Recommended choices are "cor" and "bicor", but other functions can be used as
well.
corOptions
character string giving further options to be passed to the correlation function.
networkType
character string giving network type. Allowed values are (unique abbreviations of)
"unsigned", "signed", "signed hybrid". See adjacency. power
soft-thresholding power for network construction.
verbose
integer level of verbosity. Zero means silent, higher values make the output
progressively more and more verbose.
indent
indentation for diagnostic messages. Zero means no indentation, each unit adds
two spaces.