Nothing
## ----echo=TRUE, eval=FALSE----------------------------------------------------
# install.packages("haploR", dependencies = TRUE)
## ----echo=TRUE, eval=FALSE----------------------------------------------------
# devtools::install_github("izhbannikov/haplor")
## ----echo=TRUE, message=FALSE-------------------------------------------------
library(haploR)
x <- queryHaploreg(query=c("rs10048158","rs4791078"))
x
## ----echo=TRUE, message=FALSE-------------------------------------------------
if(length(x)!=0) {
subset.high.LD <- x[as.numeric(x$r2) > 0.9, c("rsID", "r2", "chr", "pos_hg38", "is_query_snp", "ref", "alt")]
subset.high.LD
}
## ----echo=TRUE, message=FALSE, eval=FALSE-------------------------------------
# require(openxlsx)
# write.xlsx(x=subset.high.LD, file="subset.high.LD.xlsx")
## ----echo=TRUE, message=FALSE, eval=FALSE-------------------------------------
# if(length(x)!=0) {
# x[, c("Motifs", "rsID")]
# x[, c("eQTL", "rsID")]
# }
## ----echo=TRUE, message=FALSE, eval=FALSE-------------------------------------
# library(haploR)
# x <- queryHaploreg(file=system.file("extdata/snps.txt", package = "haploR"))
# x
## ----echo=TRUE, message=FALSE, eval=FALSE-------------------------------------
# library(haploR)
# # Getting a list of existing studies:
# studies <- getStudyList()
# # Let us look at the first element:
# if(!is.null(studies)) {
# studies[[1]]
# # Let us look at the second element:
# studies[[2]]
# # Query Hploreg to explore results from
# # this study:
# x <- queryHaploreg(study=studies[[1]])
# x
# }
## ----echo=TRUE, eval=FALSE, message=FALSE-------------------------------------
# library(haploR)
# tables <- getExtendedView(snp="rs10048158")
# tables
## ----echo=TRUE, message=FALSE, eval=FALSE-------------------------------------
# library(haploR)
#
# # With RsIDs:
# x <- queryRegulome(c("rs4791078","rs10048158"))
# x
#
# # With region:
# y <- queryRegulome("chr1:39492461-39492462")
# y
## ----echo=TRUE----------------------------------------------------------------
sessionInfo()
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