Description Usage Arguments Details Value Author(s) See Also
Given expression data and basic network parameters, the function calculates connectivity of each gene to a given number of nearest neighbors.
1 2 3 4 5 6 | 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)
|
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)
|
corFnc |
character string containing the name of the function to calculate correlation. Suggested
functions include |
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 ( |
nLinks |
number of links to be sampled. Should be set such that |
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. |
Connectivity of gene i
is the sum of adjacency strengths between gene i
and other genes; in
this case we take the nNeighbors
nodes with the highest connection strength to gene i
. The
adjacency strengths are calculated by correlating the given expression data using the function supplied
in corFNC
and transforming them into adjacency according to the given network type
and
power
.
A vector with one component for each gene containing the nearest neighbor connectivity.
Peter Langfelder
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