Deployed e667534 with MkDocs version: 1.5.3

index.html

@@ -296,5 +296,5 @@ <h4 class="modal-title" id="keyboardModalLabel">Keyboard Shortcuts</h4>
 
 <!--
 MkDocs version : 1.5.3
-Build Date UTC : 2024-12-15 09:04:26.306793+00:00
+Build Date UTC : 2024-12-15 09:55:50.265530+00:00
 -->

misc/tables.sh

@@ -101,6 +101,24 @@ Replication <- dplyr::mutate(replication,seqnames=as.integer(known.seqnames),pos
                dplyr::select(-known.start,-known.end,-query.seqnames,-query.start,-query.end,-seqnames,-pos)
 deCODE <- read.delim(file.path(analysis,"deCODE","deCODE.tsv"))
 UKB_PPP <- read.delim(file.path(analysis,"UKB_PPP","UKB_PPP.tsv"))
+GTEx <- read.delim(file.path(analysis,"coloc","GTEx-all.tsv")) %>%
+        dplyr::mutate(nSNP=nsnps,
+                      H0=round(H0,2),
+                      H1=round(H1,2),
+                      H2=round(H2,2),
+                      H3=round(H3,2),
+                      H4=round(H4,2)) %>%
+        dplyr::rename(Protein=prot,GeneSymbol=gene,SNPid=snpid,Tissue=qtl_id) %>%
+        dplyr::select(Protein,GeneSymbol,rsid,Tissue,nSNP,H0,H1,H2,H3,H4)
+GE <- read.delim(file.path(analysis,"coloc","eQTLCatalogue-all.tsv")) %>%
+      dplyr::mutate(nSNP=nsnps,
+                    H0=round(H0,2),
+                    H1=round(H1,2),
+                    H2=round(H2,2),
+                    H3=round(H3,2),
+                    H4=round(H4,2)) %>%
+      dplyr::rename(Protein=prot,GeneSymbol=gene,SNPid=snpid,Tissue=unique_id) %>%
+      dplyr::select(Protein,GeneSymbol,rsid,Tissue,nSNP,H0,H1,H2,H3,H4)
 dup <- read.delim(file.path(analysis,"dup","dup.tbl"))
 hs <- createStyle(textDecoration="BOLD", fontColour="#FFFFFF", fontSize=12, fontName="Arial Narrow", fgFill="#4F80BD")
 xlsx <- "https://jhz22.user.srcf.net/Caprion/results.xlsx"
@@ -111,16 +129,17 @@ writeData(wb,"Summary","Summary",xy=c(1,1),headerStyle=createStyle(textDecoratio
           fontColour="#FFFFFF", fontSize=14, fontName="Arial Narrow", fgFill="#4F80BD"))
 summary <- data.frame(Sheet=c("Protein_0.01","Protein_dr_0.01","Peptides_0.01",
                               "Protein_0.01_0.001","Protein_dr_0.01_0.001","Peptides_0.01_0.001",
-                              "Protein","Protein_dr","Peptides","Replication","deCODE","UKB_PPP","Dup"),
+                              "Protein","Protein_dr","Peptides","Replication","deCODE","UKB_PPP","GTEx","GE","Dup"),
                       Description=c("Unfiltered proteins, MAF>=0.01","DR-filtered proteins, MAF>=0.01","All peptides, MAF>=0.01",
                                     "Unfiltered proteins, MAF in (0.01,0.001]","DR-filtered proteins, MAF (0.01,0.001]",
                                     "All peptides, MAF in (0.01,0.001]",
                                     "Unfiltered proteins","DR-filtered proteins","All peptides","All/DR-filtered replication",
-                                    "deCODE replication","UKB-PPP replication","Duplicated proteins"))
+                                    "deCODE replication","UKB-PPP replication","GTEx colocalization","eQTL colocalization",
+                                    "Duplicated proteins"))
 writeDataTable(wb, "Summary", summary, xy=c(1,2), headerStyle=hs, firstColumn=TRUE, tableStyle="TableStyleMedium2")
 for (i in c("Protein_0.01","Protein_dr_0.01","Peptides_0.01",
             "Protein_0.01_0.001","Protein_dr_0.01_0.001","Peptides_0.01_0.001",
-            "Protein","Protein_dr","Peptides","Replication","deCODE","UKB_PPP","dup"))
+            "Protein","Protein_dr","Peptides","Replication","deCODE","UKB_PPP","GTEx","GE","dup"))
 {
     sheetnames <- i
     cat(sheetnames,"\n")