From 1525f161c0ba0e56f2bb62ce0a7fcb7e39b73877 Mon Sep 17 00:00:00 2001
From: "jinghuazhao@github.com" <jinghuazhao@hotmail.com>
Date: Sun, 15 Dec 2024 09:55:51 +0000
Subject: [PATCH] Deployed e667534 with MkDocs version: 1.5.3

---
 index.html     |   2 +-
 misc/tables.sh |  25 ++++++++++++++++++++++---
 sitemap.xml.gz | Bin 127 -> 127 bytes
 3 files changed, 23 insertions(+), 4 deletions(-)

diff --git a/index.html b/index.html
index 7816f94..15e61a2 100644
--- a/index.html
+++ b/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
 -->
diff --git a/misc/tables.sh b/misc/tables.sh
index 6770493..75f944b 100644
--- a/misc/tables.sh
+++ b/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")
diff --git a/sitemap.xml.gz b/sitemap.xml.gz
index d2d752f00d4b3524bc79729c367689866e8d4eb5..cef4d78d41116cce057926fa2b9bf33f1ba32b9b 100644
GIT binary patch
delta 12
Tcmb=gXOr*d;8?bNB3mT@8JYwf

delta 12
Tcmb=gXOr*d;FvXgB3mT@87>3_