getEdgelist: Create an edgelist from rpkm expression values
In mzinkgraf/fastOC: Co-expression network analysis across multiple species

Description Usage Arguments Author(s) Examples

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

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

`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

Matthew Zinkgraf, [email protected]

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