get_genomeLocFile: Import gene location files

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

Import gene location files

Description

Imports a file gene coordinate from its respective genome build.

Usage

get_genomeLocFile(
  build,
  storage_dir = tools::R_user_dir("MAGMA.Celltyping", which = "cache"),
  overwrite = FALSE
)

Arguments

build	Genome build. Must be one of: "GRCH36" : Corresponds to file "NCBI36.3.gene.loc" "GRCH37" : Corresponds to file "NCBI37.3.gene.loc" "GRCH38" : Corresponds to file "NCBI38.gene.loc"
storage_dir	Folder in which to save the file.
overwrite	Should any local files of the same name be overwritten? default TRUE.

Value

File path.

Source

## Move from data/ to Releases on GitHub to speed up MAGMA.Celltyping prefixes <- c("NCBI36.3","NCBI37.3","NCBI38") ### Made a permalink so we can always go back to this version of the data ### (even after it's been deleted from the current version). permalink_id <- "f931877dedcde103723f14242d5242fdca7b3af6" files <- stats::setNames( paste("https://github.com/neurogenomics/MAGMA_Celltyping/raw", permalink_id,"data", paste0(prefixes,".gene.loc"), sep="/"), prefixes ) local_files <- lapply(names(files), function(x){ local <- file.path(tempdir(),basename(files[x])) utils::download.file(files[x],local) return(local) }) |> `names<-`(names(files)) for(x in names(local_files)){ piggyback::pb_upload(file = local_files[[x]], repo = "neurogenomics/MAGMA_Celltyping", overwrite = TRUE) }

tmp <- MAGMA.Celltyping:::get_genomeLocFile(build = "GRCH37")

NathanSkene/MAGMA_Celltyping documentation built on Oct. 11, 2024, 7:19 a.m.