R/get_CORCES2020_hichip_fithichip_loop_calls.R

In RajLabMSSM/echoannot: echoverse module: Annotate fine-mapping results

#' FitHiChIP loop calls from human brain tissue
#'
#' FitHiChIP loop calls that overlap SNPs derived from analysis
#'  of H3K27ac HiChIP data.
#' Each row represents an individual peak identified from the feature
#' binarization analysis (see methods).
#'
#' Data originally from \href{https://doi.org/10.1038/s41588-020-00721-x}{
#' Corces et al. (bioRxiv)}, as of May 2020.
#' Specifically: \emph{STable10_Coacessibility_Peak_loop_connection},
#' \emph{HiChIP FitHiChIP Loop Calls} sheet.
#'
#' \strong{Column dictionary}
#' \describe{
#' \item{hg38_Chromosome_Anchor1}{The hg38 chromosome of the first loop Anchor.}
#' \item{hg38_Start_Anchor1}{The hg38 start position of the first loop Anchor.}
#' \item{hg38_Stop_Anchor1}{The hg38 stop position of the first loop Anchor.}
#' \item{Width_Anchor1}{The width of the first loop Anchor.}
#' \item{hg38_Chromosome_Anchor2}{
#' The hg38 chromosome of the second loop Anchor.}
#' \item{hg38_Start_Anchor2}{The hg38 start position of the second loop Anchor.}
#' \item{hg38_Stop_Anchor2}{The hg38 stop position of the second loop Anchor.}
#' \item{Width_Anchor2}{The width of the second loop Anchor.}
#' \item{Score}{The -log10(q-value) of the loop call from FitHiChIP.}
#' \item{Anchor1_hasSNP}{A boolean variable determining whether the first
#' anchor overlaps a SNP from our AD/PD GWAS analyses.}
#' \item{Anchor2_hasSNP}{A boolean variable determining whether the second
#' anchor overlaps a SNP from our AD/PD GWAS analyses.}
#' }
#' @family CORCES2020
#' @source \url{https://doi.org/10.1038/s41588-020-00721-x}
#' @examples
#' \dontrun{
#' dat <- readxl::read_excel(
#'     file.path(
#'         "~/Desktop/Fine_Mapping/echolocatoR/annotations",
#'         "Coceres_2020/STable10_Coacessibility_Peak_loop_connection.xlsx"
#'     ),
#'     skip = 19, sheet = 1
#' )
#' CORCES2020_hichip_fithichip_loop_calls <- data.table::data.table(dat)
#'
#' #### piggyback ####
#' tmp <- file.path(tempdir(), "CORCES2020_hichip_fithichip_loop_calls.tsv.gz")
#' data.table::fwrite(CORCES2020_hichip_fithichip_loop_calls, tmp, sep = "\t")
#' piggyback::pb_upload(
#'     file = tmp,
#'     repo = "RajLabMSSM/echoannot"
#' )
#' }
#' @export
get_CORCES2020_hichip_fithichip_loop_calls <- function() {
    tmp <- get_data(fname = "CORCES2020_hichip_fithichip_loop_calls.tsv.gz")
    dat <- data.table::fread(tmp, nThread = 1)
    return(dat)
}

get_CORCES2020_HiChIP_FitHiChIP_loop_calls <- function(...){
    .Deprecated("get_CORCES2020_hichip_fithichip_loop_calls")
    get_CORCES2020_hichip_fithichip_loop_calls(...)
}