enrichwrapper: Annotate the function of the cell-type-specific differential...

In yuabrahamliu/scDeconv: scDeconv is an R Package to Deconvolve Bulk DNA Methylation Data with scRNA-seq Data in a Multi-omics Manner.

Annotate the function of the cell-type-specific differential CpG sites

Description

Annotate the function of the cell-type-specific differential DNA methylation probes called from celldiff.

Usage

enrichwrapper(
  sigprobes,
  celltype,
  pairedRNA = NULL,
  pairedmethyl = NULL,
  abscut = 0.6,
  generegions = c("TSS200"),
  platform = "450K",
  uniquegenes = TRUE,
  dbs = c("GO_Biological_Process_2018", "BioPlanet_2019", "Reactome_2016"),
  write = FALSE
)

Arguments

sigprobes	The list result returned by celldiff with the inter- group differential probe selection results for each cell type.
celltype	The cell type whose differential methylation probes needs to be annotated. Should be a string of the cell type name.
pairedRNA	The RNA part of the paired RNA-DNA methylation dataset. If both this parameter and pairedmethyl are not NULL, a correlation- based method will be used to find the genes whose RNA expression level in the RNA data significantly correlated with any of the cell-type-specific differential probes in the paired methylation data, and then the enriched function of these selected genes will be analyzed and each of them will also has its individual function annotated. Should be a matrix with each column representing a sample and each row for one gene. Row names are gene symbols and column names are sample IDs. The default value is NULL, and in this case, the correlation-base method will not be used, and instead, the function annotation and enrichment analysis will be directly conducted on the cell-type-specific hyper and hypomethylated DNA methylation probes in sigprobes, with the probes mapped to corresponding genes first.
pairedmethyl	The methylation part of the paired RNA-DNA methylation dataset. If both this parameter and pairedRNA are not NULL, the correlation-based method will be used to find the genes with an expression level significantly correlated to the differential methylation probes and perform function analysis on them, while if it is NULL, the analysis will be conducted directly on the genes corresponding to the cell-type-specific differential methylation probes in sigprobes. It should be a beta value matrix with each column representing one sample and each row for a probe. Row names are probe names. Column names are sample IDs. The sample IDs should be the same as the ones in rnamat, because they are data for paired samples. Default is NULL.
abscut	When the correlation method is used to select the genes with a significant correlation to the cell-type-specific differential probes, the ones with an absolute Pearson correlation coefficient value greater than this parameter value will be selected and used for function analysis. The default value is 0.6.
generegions	When the function analysis is directly performed on the genes mapped from the differential methylated probes, if a probe located in the regions defined by this parameter, its corresponding gene will be used for the function analysis. Default is "TSS200", so that only probes within TSS200 regions will be used for gene mapping, and it can also be a vector, such as c("TSS200", "TSS1500", "1stExon"), so that probes within any of these 3 regions will be used for gene mapping. On the other hand, when the function analysis is performed on the genes significantly correlated with the changed methylation probes, actually the methylation probes are merge into gene methylation values first, and then the gene methylation values will be used to calculated the correlation with the gene RNA values in the paired RNA data. The gene methylation values are summarized according to the regions in this parameter \codgeneregions.
platform	A string indicating the platform of the differential probes recorded in sigprobes. Default is "450K", can also be "EPIC".
uniquegenes	A logical value and if this parameter is set as TRUE, after getting the genes for function analysis from the cell type indicated by celltype, these genes will be used to compare with the genes obtained similarly from other cell types recorded in sigprobes, and only the ones uniquely contained in the target cell type will be used for the downstream analysis. If this parameter is FALSE, this filter step will not be performed. Default is TRUE.
dbs	The databases for gene function enrichment analysis. Default is c("GO_Biological_Process_2018", "BioPlanet_2019", "Reactome_2016").
write	A logical value indicating whether the gene function results need to be written into txt files in the working directory. The default value is FALSE.

Value

A list with four slots recording the gene annotation and function enrichment results for the enhanced and inhibited genes (when correlation- based method is used) or for the genes mapped from the hypomethylated and hypermethylated probes (when correlation-based method is not used), and if write is TRUE, txt files will be made to save these results.

yuabrahamliu/scDeconv documentation built on March 28, 2024, 3:15 p.m.