## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) devtools::load_all(".") library(kableExtra) library(topGO) ## ----eval=FALSE--------------------------------------------------------------- # head(degenes) ## ----warning = FALSE, message = FALSE, echo=FALSE----------------------------- cut_degenes <- head(degenes) cut_degenes[, c(3, 4)] <- sapply(c(3, 4), function(x) formatC(as.numeric(cut_degenes[, x]), digits = 2, format="e")) knitr::kable(cut_degenes, row.names = FALSE) ## ----groups, warning = FALSE, message = FALSE--------------------------------- up_groups <- GeneGroups(degenes, quannumber=6) ## ----gafread, warning = FALSE, message = FALSE-------------------------------- gaf_path <- system.file("extdata", "gene_association.tair.lzma", package = "FoldGO") gaf <- GAFReader(file = gaf_path, geneid_col = 10) ## ----gaf_getters chunk 1, warning = FALSE, message = FALSE-------------------- getVersion(gaf) ## ----gaf_getters chunk 2, warning = FALSE, message = FALSE, results='hide'---- getAnnotation(gaf) ## ----annot, eval = FALSE------------------------------------------------------ # up_annotobj <- FuncAnnotGroupsTopGO(genegroups = up_groups, namespace = "MF", customAnnot = gaf, annot = topGO::annFUN.GO2genes, bggenes = bggenes) ## ----ara_annot, eval = FALSE-------------------------------------------------- # up_annotobj <- FuncAnnotGroupsTopGO(up_groups,"MF", mapping = "org.At.tair.db", annot = topGO::annFUN.org, ID = "entrez", bggenes = bggenes) ## ----human_annot, warning = FALSE, message = FALSE, results='hide'------------ up_groups <- GeneGroups(degenes_hum, quannumber=6) FuncAnnotGroupsTopGO(up_groups,"MF", mapping = "org.Hs.eg.db", annot = topGO::annFUN.org, ID = "ensembl", bggenes = bggenes_hum) ## ----fs_test, warning = FALSE, message = FALSE-------------------------------- up_fsobj <- FoldSpecTest(up_annotobj, fdrstep1 = 0.05, fdrstep2 = 0.01) down_fsobj <- FoldSpecTest(down_annotobj, fdrstep1 = 0.05, fdrstep2 = 0.01) ## ----fs_test_padj, eval=FALSE------------------------------------------------- # FoldSpecTest(up_annotobj, padjmethod = "BY") ## ----fs_table----------------------------------------------------------------- fs_table <- getFStable(up_fsobj) ## ----eval=FALSE--------------------------------------------------------------- # head(fs_table) ## ----echo=FALSE--------------------------------------------------------------- library(kableExtra) fs_table[, c(4, 5, 6, 7)] <- sapply(c(4, 5, 6, 7), function(x) formatC(as.numeric(fs_table[, x]), digits = 2, format="e")) knitr::kable(head(fs_table)) %>% kable_styling(font_size = 12) ## ----nfs_table---------------------------------------------------------------- nfs_table <- getNFStable(up_fsobj) ## ----eval=FALSE--------------------------------------------------------------- # head(nfs_table) ## ----echo=FALSE--------------------------------------------------------------- nfs_table[, c(4, 5, 6, 7)] <- sapply(c(4, 5, 6, 7), function(x) formatC(as.numeric(nfs_table[, x]), digits = 2, format="e")) knitr::kable(head(nfs_table)) %>% kable_styling(font_size = 12) ## ----fs_plot, warning = FALSE, message = FALSE, fig.height = 10, fig.width = 7---- plot(up_fsobj, down_fsobj)