get_gmt_for_gsva <- function(all_gene_sets){ gs=split(all_gene_sets$gene_symbol,all_gene_sets$gs_name) gs = lapply(gs, unique) head(gs) gsc <- GeneSetCollection(mapply(function(geneIds, keggId) { GeneSet(geneIds, geneIdType=EntrezIdentifier(), collectionType=KEGGCollection(keggId),...
我们选择一个就行,2个分组的话,其实没多大区别。 Collapse dataset to gene symbols:我们选择No_Collapse Permutation type(扰动类型):通常选择phenotype,如果样品数目较少可以选择gene_set。 Chip platform(芯片类型):如果表达gct文件的第一列为芯片探针id则此处需要选择对应的芯片平台,如果是基因symbol则无需选择。 ...
Functional KEGG categories enriched within gene sets.Travis J. WilesJ. Paul NortonColin W. RussellBrian K. DalleyKael F. FischerMatthew A. Mulvey
#step 4: retrieve gene sets for an organism from databases such as GO and KEGG: hsa_kegg_genesets <- getGenesets(org = "hsa", db = "kegg", gene.id.type = "SYMBOL", cache = TRUE, return.type="list") #step5: Parse and write the gene sets to a flat text file in GMT format...
gseaplot2可以同时可视化多个genesets。不过感觉用处不是太大。 GSEA_test <- clusterProfiler::GSEA(input_GSEA, nPerm = 1000, pvalueCutoff = 0.05, TERM2GENE = db_for_GSEA) GSEA_test_df <- as.data.frame(GSEA_test) %>% dplyr::filter(abs(NES)>1 & pvalue<0.05 & qvalues<0.25) GSEA_...
Note that this should have the same number of genes as the gene names found in the expression table. The number of samples should be the same as the number of tissue statuses. Updated gene symbols: To update the list of genes to (hopefully) find more of the genes in the KEGG pathways...
(as.character(apply(marker_cosg$names,2,head,10)))sce.Scale<-ScaleData(input_sce,features=top_10)DoHeatmap(sce.Scale,top_10)## Top3 genestop_3<-unique(as.character(apply(marker_cosg$names,2,head,3)))}symbols_list<-as.list(as.data.frame(apply(marker_cosg$names,2,head,100)))...
Although PathwayVoyager requires an internet connection in order to retrieve data from the KEGG database, all analyzes involving the provided gene sets are performed locally and no sensitive data are transmitted. This eliminates one of the major security concerns when working with confidential data ...
@sarahalshammery For your information: though I don't fully know whether the results is what you expected (only in group A (602) enriched gene sets are found), but your code as such doesn't give an error for me. See also my session info for the versions of clusterProfiler, DOSE and...
Create a list of gene sets based on KEGG pathways termsCamille TerfveXin Wang