createCytoGraph: Create Graphs of significant interactions

In umbibio/CIE-R-Package: Causal Inference and Directional Enrichment Methods on Biological Networks

Create Graphs of significant interactions

Description

Creates graphs of protein-gene interactions based on enrichment analyses by this pipeline

Usage

createCytoGraph(enrichment, ents, rels, DEGs, p.thresh=0.05,
                       fc.thresh = log(1.5), numProt=5, ids=NA,
                       numTargets=10)

Arguments

enrichment	The enrichment tables from the analysis pipeline. Can be a list of lists (multiple methods and conditions) or a list (multiple conditions, one method), or a single data frame
ents	The ents table used in the enrichment, must be a single data frame
rels	The rels table used in the enrichment, must be a single data frame
DEGs	The differentially expressed gene tables, can be a single data frame or list of data frames matching that which the pipeline was run on.
p.thresh	The p value threshold used in determining the significant differentailly expressed genes for enrichment analysis
fc.thresh	The fold count threshold used in determining the significant differentially expressed genes for enrichment analysis
numProt	The number of protiens, ranked by p.value from enrichment, to include
ids	Row indices of the regulators you wish to be included in the plot
numTargets	The number of targets of each top regulator to show. Please note that the number of targets plotted may be smaller than you expect, due to overlap.

Value

Opens a browser window with the graph, green = proteins, purple = mRNA

Examples

ChIP1ap <- filterChIPAtlas(1, NA, "auto", NA, "prostate", NA, NA, FALSE)
files <- list.files("./", ".txt")
degs <- lapply(files, function(x) {
   read.table(x, header=T, sep="\t") } )
names(degs) <- files
methods <- c("Ternary", "Quaternary", "Enrichment", "Fisher")
enrichment <- runInferenceModels(NULL, NULL, DEGs=degs,
                                method = methods,
                                ents=ChIP1ap$filteredChIP.ents,
                                rels=ChIP1ap$filteredChIP.rels,
                                useFile=F, useMart=TRUE, useBHLH=TRUE,
                                martFN="../CIE/data/mart_human_TFs.csv",
                                BHLHFN="../CIE/data/BHLH_TFs.txt")
createCytoGraph(enrichment, ChIP1ap$filteredChIP.ents,
                ChIP1ap$filteredChIP.rels, degs)

umbibio/CIE-R-Package documentation built on Sept. 26, 2023, 3:37 a.m.