Closed huerqiang closed 1 year ago
Fix https://github.com/YuLab-SMU/clusterProfiler/issues/551 KEGG api修改后, createKEGGdb也需要做响应的修改。
> > data(geneList, package="DOSE") > gene <- names(geneList)[abs(geneList) > 2] > kk <- enrichKEGG(gene = gene, + organism = 'hsa', + pvalueCutoff = 0.05, + qvalueCutoff = 0.05, + use_internal_data =T) > nrow(kk) [1] 9 > head(kk) ID Description GeneRatio BgRatio pvalue p.adjust qvalue geneID Count hsa04110 hsa04110 Cell cycle 11/94 127/8275 1.689644e-07 3.531357e-05 3.450432e-05 8318/991/9133/890/983/4085/7272/1111/891/4174/9232 11 hsa04114 hsa04114 Oocyte meiosis 10/94 131/8275 2.051606e-06 2.143928e-04 2.094797e-04 991/9133/983/4085/51806/6790/891/9232/3708/5241 10 hsa04218 hsa04218 Cellular senescence 10/94 156/8275 9.875269e-06 6.879771e-04 6.722113e-04 2305/4605/9133/890/983/51806/1111/891/776/3708 10 hsa04061 hsa04061 Viral protein interaction with cytokine and cytokine receptor 8/94 100/8275 1.622516e-05 8.477647e-04 8.283372e-04 3627/10563/6373/4283/6362/6355/9547/1524 8 hsa03320 hsa03320 PPAR signaling pathway 7/94 75/8275 2.061911e-05 8.618789e-04 8.421279e-04 4312/9415/9370/5105/2167/3158/5346 7 hsa04914 hsa04914 Progesterone-mediated oocyte maturation 7/94 102/8275 1.496049e-04 5.211236e-03 5.091815e-03 9133/890/983/4085/6790/891/5241 7
你好,请问是不是只更新了clusterProfiler4的代码,3的会不会跟进更新,谢谢,因为机器上的r没有更新到4.2,故发此问。
是的,必须安装Github上最新的版本才可以。
Fix https://github.com/YuLab-SMU/clusterProfiler/issues/551 KEGG api修改后, createKEGGdb也需要做响应的修改。