setNet: Create an igraph from genes of interest and a list of gene...

In Solatar/setR:

Description

Imports: igraph, data.table, AnnotationDbi, org.Hs.eg.db, org.Mm.eg.db

Usage

setNet(EntrezIds, sets, species, edgefactor = 1)

Arguments

EntrezIds	vector of characters or numbers, set of genes of interest
sets	list of character vectors (ENTREZIDs). This is the setlist used to connect the genes of interest.
species	character, either "human" or "mouse", must reflect the species of 'EntrezIds' and 'sets'
spread	number, factor to expand the plot

Details

it is complicated

Value

prints a plot and outputs a list: 1) a table, summarizing the hits of the genes of interest against the sets, 2) a character vector that can directly be used as input for the igraph function 'graph', 3) igraph object, the output of the igraph function 'graph', 4) a layout that can be used when ploting the output from the igraph function 'graph', 5) a vector of numbers for the edge widths in the plot

Examples

EntrezIds <- c(246329,84314,10170)
sets <- qusage::read.gmt("path/to/file.gmt")
net <- setNet(myGenes, sets, "human")

Solatar/setR documentation built on Dec. 5, 2020, 10:50 p.m.