set.pathway.catalogue: store pathway data and pre-processing

In jokergoo/CePa: Centrality-Based Pathway Enrichment

Description

store pathway data and pre-processing

Usage

set.pathway.catalogue(pathList, interactionList, mapping,
    min.node = 5, max.node = 500, min.gene = min.node, max.gene = max.node, ...)

Arguments

pathList	list of pathways
interactionList	list of interactions
mapping	a data frame or matrix providing mappings from gene id to pathway node id. The first column is node id and the second column is gene id.
min.node	minimum number of connected nodes in each pathway
max.node	maximum number of connected nodes in each pathway
min.gene	minimum number of genes in each pathway
max.gene	maximum number of genes in each pathway
...	other arguments, should have names, these data will be stored as a list member in the returned value from the function

Details

The pathway data will not be changed in the analysis, so the pathway data is integrated in one single data object by this function. Also, the function will do a little preprocess of the pathway data.

Basicly, a pathway contains a list of interactions. The pathList argument is a list where elements in the list is the vector of interaction IDs in the pathway. The interactions in the pathway can be got from a interaction list pool represented as interactionList argument. The interactionList argument stores the total interaction list in the pathway catalogue. It represents as a three columns data frame or matrix where the first column is the interaction id, the second column is the input node id and the third column is the output node id.

The mapping data frame provide the mapping from node id to gene id. The first column is the node id and the second column is the gene id.

Besides the pathList, interactionList and mapping arguments, more arguments can be added to the function. These new data will be stored as the member of the list that returned by the function. E.g., in the PID.db data, each catalogue is a pathway.catalogue object. Except the pathList, interactionList and mapping arguments, there are also node.name, node.type and version arguments.

The summary can be visualized by plot.pathway.catalogue.

Value

A pathway.catalogue class object

Author(s)

Zuguang Gu <[e-mail]>

See Also

cepa.all

Examples

## Not run: 
data(PID.db)
catalogue = set.pathway.catalogue(pathList = PID.db$NCI$pathList[1:20],
            interactionList = PID.db$NCI$intertionList, mapping = PID.db$NCI$mapping)

## End(Not run)

jokergoo/CePa documentation built on July 2, 2021, 10:28 p.m.