removePrimaryEffect: Cleaning the primary enrichment signal
In drlaguna/GPCNA: Gene Multifunctionality in Secondary Co-expression Analysis

This function generates a new expression profile by removing the primary signal of the groups of genes whose only and primary enrichment is indicated in the following parameter.

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removePrimaryEffect(expr.data, target.enrichment, net = NULL,
  significanceThreshold = 0.05, modules.to.clean = NULL,
  markers.path = NULL)

`expr.data`	The expression data to be cleaned. It can be a full path file name or a data frame with genes in columns and samples in rows.
`target.enrichment`	A string with the kind of enrichment that should be removed. This name (or list of names) should be one from the list of enrichment marker genes' files provided.
`net`	A GCN created with `createGCN` from the same expression data. It can be a full path of a file containing it or an R object. This network reflects the primary signal and it is used to determine what modules need to be cleaned in order to find the secondary signal. If no network is provided it will be created. Therefore, providing one is also a way to reduce the time spent by this function.
`significanceThreshold`	Max enrichment p-value for a module to be considred as significantly enriched.
`modules.to.clean`	List of modules to be filtered out. This parameter is NULL by default, when a list of module names is provided the significanceThreshold parameter is ignored.
`markers.path`	Folder containing user-defined lists of genes to be used as marker genes to determine modules' enrichment. This is done using WGCNA::userListEnrichment function, so they must be in a compatible format. Gene IDs must be expresed using the same format as in the expression data specified in the first parameter.

the expression data filtered that, hopefully, show the secondary role of some genes in the same format of the input expression data. The function returns NULL when no data has been filtered out.

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