Usage
nearestNeighborConnectivity(datExpr,
nNeighbors = 50, power = 6, type = "unsigned",
corFnc = "cor", corOptions = "use = 'p'",
blockSize = 1000,
sampleLinks = NULL, nLinks = 5000, setSeed = 38457,
verbose = 1, indent = 0)Arguments
datExpr
a data frame containing expression data, with rows corresponding to samples and columns
to genes. Missing values are allowed and will be ignored.
nNeighbors
number of nearest neighbors to use.
power
soft thresholding power for network construction. Should be a number greater than 1.
type
a character string encoding network type. Recognized values are (unique abbreviations of)
"unsigned", "signed", and "signed hybrid".
corFnc
character string containing the name of the function to calculate correlation. Suggested
functions include "cor" and "bicor".
corOptions
further argument to the correlation function.
blockSize
correlation calculations will be split into square blocks of this size, to prevent
running out of memory for large gene sets.
sampleLinks
logical: should network connections be sampled (TRUE) or should all
connections be used systematically (FALSE)?
nLinks
number of links to be sampled. Should be set such that nLinks * nNeighbors be
several times larger than the number of genes.
setSeed
seed to be used for sampling, for repeatability. If a seed already exists, it is saved
before the sampling starts and restored upon exit.
verbose
integer controlling the level of verbosity. 0 means silent.
indent
integer controlling indentation of output. Each unit above 0 adds two spaces.