nearestNeighborConnectivityMS: Connectivity to a constant number of nearest neighbors across multiple data sets

Description

Given expression data from several sets and basic network parameters, the function calculates connectivity of each gene to a given number of nearest neighbors in each set.

Usage

nearestNeighborConnectivityMS(multiExpr, nNeighbors = 50, power = 6, 
          type = "unsigned", corFnc = "cor", corOptions = "use = 'p'", 
          blockSize = 1000,
          sampleLinks = NULL, nLinks = 5000, setSeed = 36492,
          verbose = 1, indent = 0)

Value

A matrix in which columns correspond to sets and rows to genes; each entry contains the nearest neighbor connectivity of the corresponding gene.

Arguments

multiExpr: expression data in multi-set format. A vector of lists, one list per set. In each list there must be a component named data whose content is a matrix or dataframe or array of dimension 2 containing the expression data. Rows correspond to samples and columns to genes (probes).
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 after.
verbose: integer controlling the level of verbosity. 0 means silent.
indent: integer controlling indentation of output. Each unit above 0 adds two spaces.

Author

Peter Langfelder

Details