TDPMI

The goal of TDPMI is for time-dependent progression-related gene set enrichment analysis of myocardial infarction base on msigdbr, dplyr, stringr, ggplot2, enrichplot, clusterProfiler package.

The mfuzz package was used to cluster all the genes of each cell subgroup in myocardial infarction according to the time trend, thereby obtaining different gene modules and organizing them into a gene set annotation database. Subsequently, each gene module in the annotation database was enriched using specific gene list.

You can enter a list of genes for time-dependent progression-related gene set enrichment analysis of myocardial infarction.

Installation

You can install the TDPMI from GitHub with:

# install.packages("devtools")
devtools::install_github("mumdark/TDPMI")

Examples

You can use the code below to execute the example:

library("TDPMI")
result <- TDPMIenrich(genes=c("Aqp1","Cxcl3","Gm26870","Hba-a1","Hba-a2","Hbb-bs","Hbb-bt","Mb","mt-Atp6","mt-Atp8","mt-Co1","mt-Co2"),
                                  organism = "mmu",
                                  useFilter="TRUE",
                                  pvalueFilter=0.05,
                                  qvalueFilter=0.05,
                                  highcol="grey",
                                  lowcol="red3",
                                  typefigure="bubble")

Arguments

genes: a vector of a list of genes

pvalueFilter: pvalue filter for enrichment

qvalueFilter: qvalue filter for enrichment

highcol: color for high statistical significance

lowcol: color for low statistical significance

useFilter: Whether to filter the results based on the pvalue and qvalue

typefigure: The type of the output figure, including "barplot", "bubble" and "all"

organism: the organism of input genes (using "hsa" or "mmu")

Citation

mumdark Liu (2023). TDPMI: For time-dependent progression-related gene set enrichment analysis of myocardial infarction. https://github.com/mumdark/TDPMI