Nothing
## ----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)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.