From eeaf3c8eedfcacacaf2b655c47d163691e323031 Mon Sep 17 00:00:00 2001 From: PeteHaitch Date: Fri, 13 Oct 2023 13:13:54 +1100 Subject: [PATCH] Tweak GO terms shown - GO:0072175 (epithelial tube formation) is now row number 70 in `go.useful`. - Change is presumably due to tweaks to annotation packages - Simplest just to drop this term and to make small change to text (the broad conclusions about this cluster are unchanged). --- inst/book/cell-annotation.Rmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/inst/book/cell-annotation.Rmd b/inst/book/cell-annotation.Rmd index ae2d9c0..0735842 100644 --- a/inst/book/cell-annotation.Rmd +++ b/inst/book/cell-annotation.Rmd @@ -359,16 +359,16 @@ go.out <- goana(unique(entrez.ids[is.de]), species="Mm", # Only keeping biological process terms that are not overly general. go.out <- go.out[order(go.out$P.DE),] go.useful <- go.out[go.out$Ont=="BP" & go.out$N <= 200,] -head(go.useful[,c(1,3,4)], 40) +head(go.useful[,c(1,3,4)], 30) ``` -We see an enrichment for genes involved in lipid storage, lipid synthesis and tube formation. +We see an enrichment for genes involved in lipid storage and lipid synthesis. Given that this is a mammary gland experiment, we might guess that cluster `r chosen.text` contains luminal epithelial cells responsible for milk production and secretion. Indeed, a closer examination of the marker list indicates that this cluster upregulates milk proteins _Csn2_ and _Csn3_ (Figure \@ref(fig:violin-milk)). ```{r, echo=FALSE} # Checking that the above statements are correct. -stopifnot(c("GO:0019915", "GO:0072175", "GO:0019432") %in% head(rownames(go.useful), 40)) +stopifnot(c("GO:0019915", "GO:0019432") %in% head(rownames(go.useful), 30)) markers.nolfc <- scoreMarkers(sce.mam, lfc=0) milk <- markers.nolfc[[chosen]][c("Csn2", "Csn3"),"min.logFC.cohen"] stopifnot(all(milk > 0))