Usage
TOMsimilarityFromExpr(
datExpr,
corType = "pearson",
networkType = "unsigned",
power = 6,
TOMType = "signed",
TOMDenom = "min",
maxPOutliers = 1,
quickCor = 0,
pearsonFallback = "individual",
cosineCorrelation = FALSE,
nThreads = 0,
verbose = 1, indent = 0)
Arguments
datExpr
expression data. A data frame in which columns are genes and rows ar samples. NAs are
allowed, but not too many.
corType
character string specifying the correlation to be used. Allowed values are (unique
abbreviations of) "pearson" and "bicor", corresponding to Pearson and bidweight
midcorrelation, respectively. Missing values are handled using the
networkType
network type. Allowed values are (unique abbreviations of) "unsigned",
"signed", "signed hybrid". See adjacency. power
soft-thresholding power for netwoek construction.
TOMType
one of "none", "unsigned", "signed". If "none", adjacency
will be used for clustering. If "unsigned", the standard TOM will be used (more generally, TOM
function will receive the adjacency a
TOMDenom
a character string specifying the TOM variant to be used. Recognized values are
"min" giving the standard TOM described in Zhang and Horvath (2005), and "mean" in which
the min function in the denominator is replac
maxPOutliers
only used for corType=="bicor". Specifies the maximum percentile of data
that can be considered outliers on either
side of the median separately. For each side of the median, if
higher percentile than maxPOutliers is considered
quickCor
real number between 0 and 1 that controls the handling of missing data in the
calculation of correlations. See details.
pearsonFallback
Specifies whether the bicor calculation, if used, should revert to Pearson when median
absolute deviation (mad) is zero. Recongnized values are (abbreviations of)
"none", "individual", "all". If set to
"none", zero mad will res
cosineCorrelation
logical: should the cosine version of the correlation calculation be used? The
cosine calculation differs from the standard one in that it does not subtract the mean.
nThreads
non-negative integer specifying the number of parallel threads to be used by certain
parts of correlation calculations. This option only has an effect on systems on which a POSIX thread
library is available (which currently includes Linux and Mac OSX, but
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.