Download PTMsigDB signatures — download

Downloads and caches PTMsigDB GMT files from the Broad Institute ssGSEA2.0 repository. PTMsigDB v2.0.0 uses flanking sequences (15 amino acids centered on the phosphosite), making the analysis species-invariant within vertebrates.

Usage

download_ptmsigdb(
  species = "mouse",
  version = "v2.0.0",
  output_dir = ".",
  force_download = FALSE
)

Arguments

species: Character. Species for signatures ("mouse" or "human"). Default "mouse".
version: Character. PTMsigDB version. Default "v2.0.0".
output_dir: Character. Directory for cached files. Default current directory.
force_download: Logical. Force re-download even if cached. Default FALSE.

Value

Character path to the cached GMT file.

References

Krug et al. (2019) A Curated Resource for Phosphosite-specific Signature Analysis. Mol Cell Proteomics. doi:10.1074/mcp.TIR118.000943

Examples

if (FALSE) { # \dontrun{
gmt_path <- download_ptmsigdb(species = "mouse", output_dir = "ptmsea_cache")
pathways <- fgsea::gmtPathways(gmt_path)
} # }