getEdgelist: Create an edgelist from rpkm expression values

Description Usage Arguments Author(s) Examples

View source: R/functions.R

Description

Generate an edgelist for each gene from a list of rpkm values and return each gene and its top most correlated neighbors

Usage

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getEdgelist(rpkm, GeneMeta, top=5, weight=1,
nThreads = 2, parallel_apply=FALSE)

Arguments

rpkm

A list object where each element in the list is a data frame of rpkm values for each species

GeneMeta

Data frame that contains the project metadata. See createGeneMeta

top

An integer specifying the number of neighbors for each gene that should be printed to the edgelist. Default = 5

weight

The edge weight between genes. Default = 1

nThreads

The number of multiple threads that should be used to calculate the correlation matrix. Default = 2

parallel_apply

Logical value indicating if parRapply from parallel should be used in calulation. Default = FALSE

Author(s)

Matthew Zinkgraf, [email protected]

Examples

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data("rpkm")
rpkm_var <- filterVariance(rpkm, variance = 0.1)
GeneMeta <- createGeneMeta(rpkm_var)
gene_edgelist <- getEdgelist(rpkm_var, GeneMeta, top = 5)

mzinkgraf/fastOC documentation built on Aug. 15, 2018, 11:17 p.m.