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Supplementary notes/jp-10-4-2024/jp-10-4-2024.sh → Supplementary notes/10-4-2024/10-4-2024.sh

@@ -141,12 +141,12 @@ function forestplot()
   try(mr_single <- mr_singlesnp(dat)) #single SNP MR using Wald ratio
 
   ##save the MR results
-  exposure <- "pQTL-combined"
-  result_file0 <- paste0(".",exposure,".harmonise.txt")
-  result_file <- paste0(".",exposure,".mr.txt")
-  #result_file2 <- paste0(".",exposure,".mr_hetero.txt")
-  #result_file3 <- paste0(".",exposure,".mr_pleio.txt")
-  result_file4 <- paste0(".",exposure,".mr_single.txt")
+  exposure <- "IL6-rs2228145"
+  result_file0 <- paste0("./",exposure,".harmonise.txt")
+  result_file <- paste0("./",exposure,".mr.txt")
+  #result_file2 <- paste0("./",exposure,".mr_hetero.txt")
+  #result_file3 <- paste0("./",exposure,".mr_pleio.txt")
+  result_file4 <- paste0("./",exposure,".mr_single.txt")
   if (exists("dat")==TRUE){ write.table(dat,file=result_file0,sep="\t",col.names=T,row.names=F,quote=F)}
   if (exists("mr_results")==TRUE){ write.table(mr_results,file=result_file,sep="\t",col.names=T,row.names=F,quote=F)}
   #if (exists("mr_hetero")==TRUE){ write.table(mr_hetero,file=result_file2,sep="\t",col.names=T,row.names=F,quote=F)}

Supplementary notes/10-4-2024/IL6-rs2228145.harmonise.txt

@@ -0,0 +1,5 @@
+SNP	effect_allele.exposure	other_allele.exposure	effect_allele.outcome	other_allele.outcome	beta.exposure	beta.outcome	eaf.exposure	eaf.outcome	remove	palindromic	ambiguous	id.outcome	se.outcome	pval.outcome	outcome	mr_keep.outcome	pval_origin.outcome	se.exposure	pval.exposure	exposure	mr_keep.exposure	pval_origin.exposure	id.exposure	action	mr_keep	samplesize.outcome
+rs2228145	A	C	A	C	-0.1684	-0.0389	NA	NA	FALSE	FALSE	FALSE	95T3mQ	0.0052	4.802e-14	Coronary artery disease	TRUE	reported	0.0119	1.83439e-45	IL-6	TRUE	reported	NyZipD	2	TRUE	NA
+rs2228145	A	C	A	C	-0.1684	-0.07696	NA	NA	FALSE	FALSE	FALSE	fX8wHD	0.01418	3.5e-09	Rheumatoid arthritis	TRUE	reported	0.0119	1.83439e-45	IL-6	TRUE	reported	NyZipD	2	TRUE	NA
+rs2228145	A	C	A	C	-0.1684	0.07637	NA	NA	FALSE	FALSE	FALSE	iSqC6k	0.01716	8.67e-06	Atopic dermatitis	TRUE	reported	0.0119	1.83439e-45	IL-6	TRUE	reported	NyZipD	2	TRUE	NA
+rs2228145	A	C	A	C	-0.1684	-0.0001508	NA	NA	FALSE	FALSE	FALSE	wA3yAp	0.001067	0.8876	Abdominal aortic aneurysm	TRUE	reported	0.0119	1.83439e-45	IL-6	TRUE	reported	NyZipD	2	TRUE	NA

Supplementary notes/10-4-2024/IL6-rs2228145.mr.txt

@@ -0,0 +1 @@
+

Supplementary notes/10-4-2024/IL6-rs2228145.mr_single.txt

@@ -0,0 +1,13 @@
+exposure	outcome	id.exposure	id.outcome	samplesize	SNP	b	se	p
+IL-6	Coronary artery disease	NyZipD	95T3mQ	NA	rs2228145	0.230997624703088	0.0308788598574822	7.38888279689088e-14
+IL-6	Coronary artery disease	NyZipD	95T3mQ	NA	All - Inverse variance weighted	NA	NA	NA
+IL-6	Coronary artery disease	NyZipD	95T3mQ	NA	All - MR Egger	NA	NA	NA
+IL-6	Rheumatoid arthritis	NyZipD	fX8wHD	NA	rs2228145	0.457007125890736	0.0842042755344418	5.7192901117009e-08
+IL-6	Rheumatoid arthritis	NyZipD	fX8wHD	NA	All - Inverse variance weighted	NA	NA	NA
+IL-6	Rheumatoid arthritis	NyZipD	fX8wHD	NA	All - MR Egger	NA	NA	NA
+IL-6	Atopic dermatitis	NyZipD	iSqC6k	NA	rs2228145	-0.453503562945368	0.101900237529691	8.56840789294565e-06
+IL-6	Atopic dermatitis	NyZipD	iSqC6k	NA	All - Inverse variance weighted	NA	NA	NA
+IL-6	Atopic dermatitis	NyZipD	iSqC6k	NA	All - MR Egger	NA	NA	NA
+IL-6	Abdominal aortic aneurysm	NyZipD	wA3yAp	NA	rs2228145	0.000895486935866983	0.00633610451306413	0.887608591980919
+IL-6	Abdominal aortic aneurysm	NyZipD	wA3yAp	NA	All - Inverse variance weighted	NA	NA	NA
+IL-6	Abdominal aortic aneurysm	NyZipD	wA3yAp	NA	All - MR Egger	NA	NA	NA

index.html

@@ -297,5 +297,5 @@ <h4 class="modal-title" id="keyboardModalLabel">Keyboard Shortcuts</h4>
 </html>
 <!--
 MkDocs version : 1.5.3
-Build Date UTC : 2024-04-11 15:51:11.706060+00:00
+Build Date UTC : 2024-04-11 15:56:43.145328+00:00
 -->

rsid/jp-10-4-2024/jp-10-4-2024.sh → rsid/10-4-2024/10-4-2024.sh

@@ -141,12 +141,12 @@ function forestplot()
   try(mr_single <- mr_singlesnp(dat)) #single SNP MR using Wald ratio
 
   ##save the MR results
-  exposure <- "pQTL-combined"
-  result_file0 <- paste0(".",exposure,".harmonise.txt")
-  result_file <- paste0(".",exposure,".mr.txt")
-  #result_file2 <- paste0(".",exposure,".mr_hetero.txt")
-  #result_file3 <- paste0(".",exposure,".mr_pleio.txt")
-  result_file4 <- paste0(".",exposure,".mr_single.txt")
+  exposure <- "IL6-rs2228145"
+  result_file0 <- paste0("./",exposure,".harmonise.txt")
+  result_file <- paste0("./",exposure,".mr.txt")
+  #result_file2 <- paste0("./",exposure,".mr_hetero.txt")
+  #result_file3 <- paste0("./",exposure,".mr_pleio.txt")
+  result_file4 <- paste0("./",exposure,".mr_single.txt")
   if (exists("dat")==TRUE){ write.table(dat,file=result_file0,sep="\t",col.names=T,row.names=F,quote=F)}
   if (exists("mr_results")==TRUE){ write.table(mr_results,file=result_file,sep="\t",col.names=T,row.names=F,quote=F)}
   #if (exists("mr_hetero")==TRUE){ write.table(mr_hetero,file=result_file2,sep="\t",col.names=T,row.names=F,quote=F)}

rsid/10-4-2024/IL6-rs2228145.harmonise.txt

@@ -0,0 +1,5 @@
+SNP	effect_allele.exposure	other_allele.exposure	effect_allele.outcome	other_allele.outcome	beta.exposure	beta.outcome	eaf.exposure	eaf.outcome	remove	palindromic	ambiguous	id.outcome	se.outcome	pval.outcome	outcome	mr_keep.outcome	pval_origin.outcome	se.exposure	pval.exposure	exposure	mr_keep.exposure	pval_origin.exposure	id.exposure	action	mr_keep	samplesize.outcome
+rs2228145	A	C	A	C	-0.1684	-0.0389	NA	NA	FALSE	FALSE	FALSE	95T3mQ	0.0052	4.802e-14	Coronary artery disease	TRUE	reported	0.0119	1.83439e-45	IL-6	TRUE	reported	NyZipD	2	TRUE	NA
+rs2228145	A	C	A	C	-0.1684	-0.07696	NA	NA	FALSE	FALSE	FALSE	fX8wHD	0.01418	3.5e-09	Rheumatoid arthritis	TRUE	reported	0.0119	1.83439e-45	IL-6	TRUE	reported	NyZipD	2	TRUE	NA
+rs2228145	A	C	A	C	-0.1684	0.07637	NA	NA	FALSE	FALSE	FALSE	iSqC6k	0.01716	8.67e-06	Atopic dermatitis	TRUE	reported	0.0119	1.83439e-45	IL-6	TRUE	reported	NyZipD	2	TRUE	NA
+rs2228145	A	C	A	C	-0.1684	-0.0001508	NA	NA	FALSE	FALSE	FALSE	wA3yAp	0.001067	0.8876	Abdominal aortic aneurysm	TRUE	reported	0.0119	1.83439e-45	IL-6	TRUE	reported	NyZipD	2	TRUE	NA

rsid/10-4-2024/IL6-rs2228145.mr.txt

@@ -0,0 +1 @@
+

rsid/10-4-2024/IL6-rs2228145.mr_single.txt

@@ -0,0 +1,13 @@
+exposure	outcome	id.exposure	id.outcome	samplesize	SNP	b	se	p
+IL-6	Coronary artery disease	NyZipD	95T3mQ	NA	rs2228145	0.230997624703088	0.0308788598574822	7.38888279689088e-14
+IL-6	Coronary artery disease	NyZipD	95T3mQ	NA	All - Inverse variance weighted	NA	NA	NA
+IL-6	Coronary artery disease	NyZipD	95T3mQ	NA	All - MR Egger	NA	NA	NA
+IL-6	Rheumatoid arthritis	NyZipD	fX8wHD	NA	rs2228145	0.457007125890736	0.0842042755344418	5.7192901117009e-08
+IL-6	Rheumatoid arthritis	NyZipD	fX8wHD	NA	All - Inverse variance weighted	NA	NA	NA
+IL-6	Rheumatoid arthritis	NyZipD	fX8wHD	NA	All - MR Egger	NA	NA	NA
+IL-6	Atopic dermatitis	NyZipD	iSqC6k	NA	rs2228145	-0.453503562945368	0.101900237529691	8.56840789294565e-06
+IL-6	Atopic dermatitis	NyZipD	iSqC6k	NA	All - Inverse variance weighted	NA	NA	NA
+IL-6	Atopic dermatitis	NyZipD	iSqC6k	NA	All - MR Egger	NA	NA	NA
+IL-6	Abdominal aortic aneurysm	NyZipD	wA3yAp	NA	rs2228145	0.000895486935866983	0.00633610451306413	0.887608591980919
+IL-6	Abdominal aortic aneurysm	NyZipD	wA3yAp	NA	All - Inverse variance weighted	NA	NA	NA
+IL-6	Abdominal aortic aneurysm	NyZipD	wA3yAp	NA	All - MR Egger	NA	NA	NA