map_snps_to_genes

[ushagogal]

1. I am currently attempting to run the map_snps_to_genes function in R. In addition, the MAGMA_Celltyping package is not loading in my R session, which could contribute to my error.

This is the command that I put into R. map_snps_to_genes( path_formatted, genome_build = NULL, upstream_kb = 35, downstream_kb = 10, N = NULL, duplicate = c("drop", "first", "last", "error"), synonym_dup = c("skip", "skip-dup", "drop", "drop-dup", "error"), genome_ref_path = NULL, population = "eur", genes_only = FALSE, storage_dir = tools::R_user_dir("MAGMA.Celltyping", which = "cache"), force_new = FALSE, version = NULL, verbose = TRUE )

Console output

#Error in map_snps_to_genes(path_formatted, genome_build = NULL, upstream_kb = 35,  : 
  could not find function "map_snps_to_genes"

Expected behaviour

If working properly, I expect the function to be a genes.raw file about which SNPs map to which genes based on the provided parameters.

[Al-Murphy]

I would say you need to library(MAGMA.Celltyping) first or use MAGMA.Celltyping::map_snps_to_genes, R doesn't know where to find the function in your current set up