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)
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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, Matthew.Zinkgraf@wwu.edu
1 2 3 4 | data("rpkm")
rpkm_var <- filterVariance(rpkm, variance = 0.1)
GeneMeta <- createGeneMeta(rpkm_var)
gene_edgelist <- getEdgelist(rpkm_var, GeneMeta, top = 5)
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