go_multinomial: Run GO analysis over methylation sets with multi-class...
In ZhenWei10/m6ALogisticModel: Linear model analysis on RNA modification data.

go_multinomial is a function used to run GO analysis on multi-class labeled ranged data. The back ground used is the shared genes in all of the ranges.

go_multinomial(Y, row_ranges, txdb, orgDb, HDER = "GO_multinomial",
  category = "BP", gene_key = "ENTREZID", min_bg_count = 10,
  min_gs_count = 10, max_bg_count = 500, max_gs_count = 500,
  pvalue_correction = "BH", GO_Slim = FALSE, EASE_Score = TRUE,
  top_terms = 10, save_chart = FALSE, background_ranges = NULL)

`Y`	A `vector` that defines the observed multinomial response variable.
`row_ranges`	A `GRanges` object that defines the genomic location of each sites on genome.
`txdb`	A `txdb` object downloaded from bioconductor.
`orgDb`	An `OrgDb` object defined by AnnotationDbi.
`HDER`	A `character` defining the subtitle and the file name of the plot.
`category`	A character specifying the gene ontology category, can be one of "BP", "CC", and "MF", default "BP".
`gene_key`	A character specifying the type of the gene ID, the available types of the keys can be find using `keytypes(org.Hs.eg.db)`, default "ENTREZID".
`min_bg_count`	Term minimum number of occurence in background genes; default 10.
`min_gs_count`	Term minimum number of occurence in gene set genes; default 10.
`max_bg_count`	Term maximum number of occurence in background genes; default 500.
`max_gs_count`	Term maximum number of occurence in gene set genes; default 500.
`pvalue_correction`	Method used for multiple hypothesis adjustment, can be one in "holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr", and "none".
`GO_Slim`	Whether to conduct enrichment analysis only on GO slim terms (a certain subset to GO terms), default FALSE.
`EASE_Score`	Whether or not use EASE score method. (a more conservative hypergeomatric test calculation used in DAVID) for more details please refer to here, default TRUE.
`top_terms`	Top number of terms (sorted by p values) for each multinomial class returned in the analysis, default is 10.
`save_chart`	Whether to save the chart of GO enrichment for each calss, default FALSE.
`background_ranges`	A `GRanges` object that defines the GO enrichment background, default is not used.