Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
echo=TRUE,
progress =FALSE,
comment = "#>"
)
options(rmarkdown.html_vignette.check_title = FALSE)
## ---- colocalization_framework.png, fig.align = 'center', out.width = "70%", echo=FALSE----
# knitr::include_graphics("images/quick_start/colocalization_framework.png")
## ---- results = 'hide', echo=TRUE, message=FALSE, warning=FALSE, eval=FALSE----
# library(data.table)
# library(xQTLbiolinks)
# library(stringr)
# library(coloc)
## ---- message=FALSE, warning=FALSE, include=FALSE-----------------------------
temp1 <- tempfile(fileext=".zip")
download.file("http://bioinfo.szbl.ac.cn/xQTL_biolinks/xqtl_data/env_new.zip", temp1)
load(unz(temp1,"env_new.RData"))
close(file(temp1))
rm(temp1)
## ---- results = 'hide', echo=TRUE, message=FALSE, warning=FALSE, eval=FALSE----
# gwasDF <- fread("http://bioinfo.szbl.ac.cn/xQTL_biolinks/xqtl_data/gwasDFsub.txt")
# tissueSiteDetail="Brain - Cerebellum"
## ---- eval=TRUE---------------------------------------------------------------
head(gwasDF)
## ---- results = 'hide', echo=TRUE, message=FALSE, warning=FALSE, eval=FALSE----
# sentinelSnpDF <- xQTLanalyze_getSentinelSnp(gwasDF, pValueThreshold = 5e-08)
## ---- eval=TRUE---------------------------------------------------------------
sentinelSnpDF
## ---- results = 'hide', echo=TRUE, message=FALSE, warning=FALSE, eval=FALSE----
# traitsAll <- xQTLanalyze_getTraits(sentinelSnpDF, detectRange=1e6, tissueSiteDetail=tissueSiteDetail)
## ---- eval=TRUE---------------------------------------------------------------
traitsAll
## ---- results = 'hide', echo=TRUE, message=FALSE, warning=FALSE, eval=FALSE----
# output <- xQTLanalyze_coloc(gwasDF, "ENSG00000109684", tissueSiteDetail=tissueSiteDetail) # using gene symbol
## ---- eval=TRUE---------------------------------------------------------------
output$coloc_Out_summary
## ---- results = 'hide', echo=TRUE, message=FALSE, warning=FALSE, eval=FALSE----
# outputs <- rbindlist(lapply( unique(traitsAll$gencodeId), function(x){ # using gencode ID.
# xQTLanalyze_coloc(gwasDF, x, tissueSiteDetail=tissueSiteDetail, method = "Both")$colocOut }))
## ---- eval=TRUE---------------------------------------------------------------
outputs
## ---- results = 'hide', echo=TRUE, message=FALSE, warning=FALSE, eval=FALSE----
# xQTLvisual_eqtl("ENSG00000109684")
## ---- eqtl_multiple_tissues, fig.align = 'center', out.width = "80%", echo=FALSE----
# knitr::include_graphics("images/quick_start/eQTL_multiple_tissue.png")
## ---- results = 'hide', echo=TRUE, message=FALSE, warning=FALSE, eval=FALSE----
# eqtlAsso <- xQTLdownload_eqtlAllAsso(gene="ENSG00000109684",
# tissueLabel = tissueSiteDetail)
# gwasEqtldata <- merge(gwasDF, eqtlAsso[,.(rsid=snpId, position=pos, maf, pValue)],
# by=c("rsid", "position"), suffixes = c(".gwas",".eqtl"))
## ---- results = 'hide', echo=TRUE, message=FALSE, warning=FALSE, eval=FALSE----
# xQTLvisual_locusCompare(gwasEqtldata[,.(rsid, pValue.eqtl)],
# gwasEqtldata[,.(rsid, pValue.gwas)], legend_position = "bottomright")
## ---- compare.png, fig.align = 'center', out.width = "50%", echo=FALSE--------
# knitr::include_graphics("images/quick_start/compare.png")
## ---- results = 'hide', echo=TRUE, message=FALSE, warning=FALSE, eval=FALSE----
# xQTLvisual_locusZoom(gwasEqtldata[,.(rsid, chrom, position, pValue.gwas)], legend=FALSE)
## ---- gwas_legendF.png, fig.align = 'center', out.width = "50%", echo=FALSE----
# knitr::include_graphics("images/quick_start/gwas_legendF.png")
## ---- results = 'hide', echo=TRUE, message=FALSE, warning=FALSE, eval=FALSE----
# xQTLvisual_locusZoom(gwasEqtldata[,.(rsid, chrom, position, pValue.eqtl)],
# highlightSnp = "rs13120565", legend=FALSE)
## ---- eqtl_legendF.png, fig.align = 'center', out.width = "50%", echo=FALSE----
# knitr::include_graphics("images/quick_start/eqtl_legendF.png")
## ---- results = 'hide', echo=TRUE, message=FALSE, warning=FALSE, eval=FALSE----
# xQTLvisual_eqtlExp("rs13120565", "ENSG00000109684", tissueSiteDetail = tissueSiteDetail)
## ---- exp.png, fig.align = 'center', out.width = "45%", echo=FALSE------------
# knitr::include_graphics("images/quick_start/exp.png")
## ---- results = 'hide', echo=TRUE, message=FALSE, warning=FALSE, eval=FALSE----
# xQTLvisual_locusCombine(gwasEqtldata[,c("rsid","chrom", "position", "pValue.gwas", "pValue.eqtl")],
# highlightSnp="rs13120565")
## ---- xQTLvisual_locusCombine.png, fig.align = 'center', out.width = "90%", echo=FALSE----
# knitr::include_graphics("images/quick_start/xQTLvisual_locusCombine.png")
## ---- results = 'hide', echo=TRUE, message=FALSE, warning=FALSE, eval=FALSE----
# multi_tissue_coloc <- xQTLvisual_coloc(gene="ENSG00000109684", variantName="rs13120565",
# tissueLabels = c("Brain - Cerebellar Hemisphere",
# "Brain - Cerebellum", "Thyroid", "Lung",
# "Cells - EBV-transformed lymphocytes"))
## ---- propensity.png, fig.align = 'center', out.width = "70%", echo=FALSE-----
# knitr::include_graphics("images/quick_start/propensity.png")
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.