getModulesEnrichment: Modules enrichment
In drlaguna/GPCNA: Gene Multifunctionality in Secondary Co-expression Analysis

This function determine the module enrichment of a GCN

1 2	getModulesEnrichment(net, markers.path = ".", return.processed = F, significanceThreshold = 1, outputCorrectedPvalues = T, debug = F)

`net`	A GCN created with `createGCN`. It can be an R object or the full path of a file containing it. If a filename is provided this function will first look for a file with the same name but ending in ".enrichment.csv". If the file exists the function will return its content.
`markers.path`	Folder containing user-defined lists of genes to be used as marker genes to determine modules enrichment. They must have in the first row the name of the enrichment and then, a gene ID on every row. Gene IDs must be expresed using the same format as in the network specified in the first parameter.
`return.processed`	When True the functions returns the -log10 of the p-value obtained replacing the -inf values by the highest value obtained. When False the function returns the p-values. This parameter is False by default.
`significanceThreshold`	When this value is lower than 1 this function returns the name of the celltype enrichment of each module which is exclusively enriched by a single celltype with a p-value lower than the value received by this parameter. In this case, the value of return.processed is ignored.
`outputCorrectedPvalues`	When true some corrections are made to the standard fisher test obtained. Firstly a Bonferroni correction, then a regression correctio to reduce bias of using too big enrichment sets. This paremeter is True by default.
`debug`	Show some messages about the test made

a matrix with a column for each module in the network and a row for each enrichment type. Values in the matrix reflects the p-value resulting from the test made to determine if the module is enriched or not. Alternatively, when significanceThreshold < 1 a named vector with the enrichment name for each module significantly and exclusivelly enriched by a celltype.

drlaguna/GPCNA documentation built on Sept. 22, 2020, 11:47 p.m.