clusterProfiler introduction failed, 发布之日即是死亡之日
这篇旧博客写的本是一篇介绍 clusterProfiler 的文章失效的事,但我后来整理时回想起来我以前说过的一句话:
The day a research project is published shouldn’t be the day it’s dead.
Original post: use clusterProfiler as an universal enrichment analysis tool
But things allways change
data link broke
http://www.disgenet.org/ds/DisGeNET/results/all_gene_disease_associations.tar.gz should be replaced by http://www.disgenet.org/ds/DisGeNET/results/all_gene_disease_associations.tsv.gz
use
tibble::as_tibble()
instead ofDOSE::summary()
: Warning message::summary(edn) : In DOSE summary method to convert the object to data.frame is deprecated, please use as.data.frame instead.
clusterProfiler::GSEA()
failed
Following is updated code:
data("geneList", package = 'DOSE');
<- geneList %>% {names(.)[abs(.) > 2]};
deg
<- readr::read_tsv('all_gene_disease_associations.tsv.gz');
agda <- dplyr::select(agda, 'diseaseId', 'geneId');
disease2gene <- dplyr::select(agda, 'diseaseId', 'diseaseName');
disease2name
<- clusterProfiler::enricher(deg, TERM2GENE = disease2gene, TERM2NAME = disease2name);
e ::as_tibble(e);
tibble
:::barplot.enrichResult(e);
DOSE::dotplot(e);
DOSE::enrichMap(e);
DOSE
<- clusterProfiler::GSEA(geneList, TERM2GENE = disease2gene, TERM2NAME = disease2name);
g ::as_tibble(g) tibble