quickBar: quickBar

In Krutik6/TimiRGeN: Time sensitive microRNA-mRNA integration, analysis and network generation tool

quickBar

Description

Creates a bar plot which compares the confidence levels for each wikipathway association to the filtered input data. The number of genes in common between a pathway and the input data are taken into account to generate confidence scores. This function is used specifically for a single time point at a time, or if using "s" analysis, the function is used for a single time point within a single gene type (miR or mRNA).

Usage

quickBar(X, Y, N)

Arguments

X	Dataframes within a list including count information, confidence scores and wikipathway information. This is the output from the enrichWiki function. It will be stored as metadata within the MAE used in the enrichWiki function. Data can be retrieved using [[i]][[j]] on the output of enrichWiki.
Y	String which is associated to the nested dataframe selected for X. This is the output from the enrichWiki function. It will be stored as metadata within the MAE used in the enrichWiki function. Data can be retrieved using names([[i]][j]) on the output of enrichWiki.
N	Integer representing number of pathways to display. Default is 15.

Value

Bar plot showing which pathways are most enriched for genes found at each time point ("c") or at each time point within a gentype ("s").

Examples

library(org.Mm.eg.db)

MAE <- MultiAssayExperiment()

metadata(MAE)[["e_list"]] <- e_list_mouse

MAE <- dloadGmt(MAE, species = "Mus musculus")

MAE <- enrichWiki(MAE = MAE, method = 'c', ID_list = metadata(MAE)[[1]],
                   orgDB = org.Mm.eg.db, path_gene = assay(MAE, 1),
                   path_name = assay(MAE, 2), ID = "ENTREZID",
                   universe = assay(MAE, 1)[[2]])

q <- quickBar(X = metadata(MAE)[[2]][[1]], Y = names(metadata(MAE)[[2]][1]))

# to view bar plot enter plot(q)

Krutik6/TimiRGeN documentation built on Jan. 27, 2024, 7:46 p.m.