{"id":46,"date":"2021-10-18T00:24:47","date_gmt":"2021-10-17T16:24:47","guid":{"rendered":"https:\/\/linguopeng.top\/?p=46"},"modified":"2024-06-24T23:44:25","modified_gmt":"2024-06-24T15:44:25","slug":"clusterprofiler","status":"publish","type":"post","link":"https:\/\/linguopeng.top\/?p=46","title":{"rendered":"clusterProfiler"},"content":{"rendered":"\n
#BiocManager::install('clusterProfiler')\n#BiocManager::install(\"pathview\")\n#install.packages('tidyverse')\nlibrary(clusterProfiler)\nlibrary(tidyverse)\ndata1<-read.table(\"K2.txt\",header = TRUE,row.names = 1)\n#head(data1)<\/code><\/pre>\n\n\n\n
\"\"<\/div><\/figure>\n\n\n\n
data1.2<-data1 %>% select_if(is.numeric)\ndata1.2$Group <- factor(data1$Group,levels=c(\"CCFM16\",\"Placebo\"))\n#write.csv(data1.2,\"data1.2.csv\")\n#summary(data1.2)\n'''\nshapiro.test\u7684\u96f6\u5047\u8bbe\u662f\u53d8\u91cf\u7b26\u5408\u6b63\u6001\u5206\u5e03\uff0c\n\u5f53\u7ed3\u679c\u7684p-value > 0.05\u65f6\uff0c\u4e0d\u80fd\u62d2\u7edd\u539f\u5047\u8bbe\uff0c\u8868\u660e\u53d8\u91cf\u670d\u4ece\u6b63\u6001\u5206\u5e03\ndim(data1)\ndiff_test <- data1 %>% \n    select_if(is.numeric) \nshapiro.test(diff_test[,1])\nShapiro-Wilk normality test\ndata:  diff_test[, 1]\nW = 0.97972, p-value = 0.297\n'''\n##  \u7b26\u5408\u6b63\u6001\u5206\u5e03\uff0c\u5219\u8fdb\u884ct-test\ndiff <- data1.2 %>% \n  select_if(is.numeric) %>%\n  map_df(~ broom::tidy(t.test(. ~ Group,data = data1.2)), .id = 'var')\n#\u6574\u5408\u6570\u636e\ndiff$q.value <- p.adjust(diff$p.value,\"fdr\")\ndiff$FC<-diff$estimate1\/diff$estimate2\ndiff$logFC<-log2(diff$FC)\np1<-diff[,c(1,14,6)]\nnewdata1<-na.omit(p1)\n#newdata2  <- filter(newdata1, newdata$logFC!= Inf)\n#newdata3  <- filter(newdata2, newdata$logFC = Inf)\np2 <- p1[p1$logFC!= \"-Inf\",]\np3 <- p2[p2$logFC!= \"Inf\",]\nwrite.csv(newdata3,\"p1.csv\")\n#diff <- diff %>% filter(p.value < 0.05)\n##################UP###############\nflt <- p3[p3$logFC > 1.1 & p3$p.value < 0.05,]\nup_gene<-na.omit(flt)<\/code><\/pre>\n\n\n\n
\"\"<\/div><\/figure>\n\n\n\n
library(\"pathview\")\nlibrary(clusterProfiler)\nekegg <- enrichKEGG(gene =up_gene$var,\n                    organism = \"ko\",\n                    keyType = \"kegg\")\nView(as.data.frame(ekegg))              \ndotplot(ekegg)<\/code><\/pre>\n\n\n\n
\"\"<\/div><\/figure>\n\n\n\n
#browseKEGG(ekegg, \"rno05146\")\nbarplot(ekegg, showCategory = 20)<\/code><\/pre>\n\n\n\n
\"\"<\/div><\/figure>\n\n\n\n
dotplot(ekegg, x = \"GeneRatio\",\n        color = \"p.adjust\", \n        showCategory = 30, \n        split = NULL, font.size = 12,)<\/code><\/pre>\n\n\n\n
\"\"<\/div><\/figure>\n\n\n\n
browseKEGG(ekegg, \"ko02025\")\n#################down##########\nflt <- p3[p3$logFC < 1.1 & p3$p.value < 0.05,]\ndown_gene<-na.omit(flt)\nlibrary(\"pathview\")\nlibrary(clusterProfiler)\nekegg <- enrichKEGG(gene =down_gene$var,\n                    organism = \"ko\",\n                    keyType = \"kegg\")\nView(as.data.frame(ekegg))              \ndotplot(ekegg)<\/code><\/pre>\n\n\n\n
\"\"<\/div><\/figure>\n\n\n\n
dotplot(ekegg, x = \"GeneRatio\",\n        color = \"p.adjust\", \n        showCategory = 30, \n        split = NULL, font.size = 12,)<\/code><\/pre>\n\n\n\n
\"\"<\/div><\/figure>\n\n\n\n
browseKEGG(ekegg, \"ko00720\")<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[8],"tags":[3],"class_list":["post-46","post","type-post","status-publish","format-standard","hentry","category-r","tag-r"],"_links":{"self":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/46","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=46"}],"version-history":[{"count":3,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/46\/revisions"}],"predecessor-version":[{"id":662,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/46\/revisions\/662"}],"wp:attachment":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=46"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=46"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=46"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}