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pval__appetite_regulatory_hormones.R

+# setwd("/home/gdevailly/work/project/rosepigs/rosepigs")
+library(data.table)
+library(rtracklayer)
+library(tximport)
+library(stringr)
+library(ggplot2)
+library(readr)
+library(dplyr)
+library(visNetwork)
+library(purrr)
+
+# load a gtf file
+gtf <- import(con = "data/Sus_scrofa.Sscrofa11.1.102.gtf.gz", format = "GFF")
+
+# load a txi table
+load("data/txi.RData")
+
+# csv file with appetite regulating hormones
+reacto <- read_tsv("data/Participating Molecules [R-HSA-400508].tsv")
+
+
+genes <- gtf[gtf$type == "gene", ]
+table(reacto$Name %in% genes$gene_name)
+
+genes[genes$gene_id == "genes", ]
+
+
+nodes <- left_join(reacto, as.data.frame(mcols(genes)[, c("gene_id", "gene_name")]), by = c("Name" = "gene_name"))
+
+
+nodes_m_fas <- txi$abundance[rownames(txi$abundance) %in% nodes$gene_id, metadata$line == "G11-" & metadata$condition == "fasted"]
+nodes_m_fed <- txi$abundance[rownames(txi$abundance) %in% nodes$gene_id, metadata$line == "G11-" & metadata$condition == "fed"   ]
+nodes_p_fas <- txi$abundance[rownames(txi$abundance) %in% nodes$gene_id, metadata$line == "G11+" & metadata$condition == "fasted"]
+nodes_p_fed <- txi$abundance[rownames(txi$abundance) %in% nodes$gene_id, metadata$line == "G11+" & metadata$condition == "fed"   ]
+
+# applicate student test for G11-
+nodes_m <- cbind(
+    nodes,
+    map_dfr(nodes$gene_id, function(x) {
+        if(is.na(x)) return(tibble(log2fc = NA, pval = NA))
+        tibble(
+            log2fc = log2(median(nodes_m_fed[x, ], na.rm = TRUE) / median(nodes_m_fas[x, ], na.rm = TRUE)),
+            pval = t.test(nodes_m_fed[x, ], nodes_m_fas[x, ])$p.value	
+        )
+    })
+)
+
+# applicate student test for G11+
+nodes_p <- cbind(
+    nodes,
+    map_dfr(nodes$gene_id, function(x) {
+        if(is.na(x)) return(tibble(log2fc = NA, pval = NA))
+        tibble(
+            log2fc = log2(median(nodes_p_fed[x, ], na.rm = TRUE) / median(nodes_p_fas[x, ], na.rm = TRUE)),
+            pval = t.test(nodes_p_fed[x, ], nodes_p_fas[x, ])$p.value	
+        )
+    })
+)
+
+
+# adjust the pvalues with with FDR method
+nodes_m$adjpval <- p.adjust(nodes_m$pval, method = "fdr")
+nodes_p$adjpval <- p.adjust(nodes_p$pval, method = "fdr")
+