Read a polygenic scoring file — read_scoring

This function imports a PGS scoring file. For more information about the scoring file schema check vignette("pgs-scoring-file", package = "quincunx").

Usage

read_scoring_file(
  source,
  harmonized = FALSE,
  assembly = c("GRCh38", "GRCh37"),
  protocol = "http",
  metadata_only = FALSE
)

Arguments

source: PGS scoring file. This can be specified in three forms: (i) a PGS identifier, e.g. "PGS000001", (ii) a path to a local file, e.g. "~/PGS000001.txt" or "~/PGS000001.txt.gz" or (iii) a direct URL to the PGS Catalog FTP server, e.g. "http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000001/ScoringFiles/PGS000001.txt.gz".
harmonized: Whether to read an alternative, harmonized version of the PGS scoring file. This version contains harmonized variant information. This information is provided in extra columns whose names are prefixed with "hm_".
assembly: If harmonized is TRUE, assembly indicates which the genome assembly to choose for the harmonized variant data. assembly must be either "GRCh38" (default) or "GRCh37".
protocol: Network protocol for communication with the PGS Catalog FTP server: either "http" or "ftp".
metadata_only: Whether to read only the comment block (header) from the scoring file.

Value

The returned value is a named list. The names are copied from the arguments passed in source. Each element of the list contains another list of two elements: "metadata" and "data". The "metadata" element contains data parsed from the header of the PGS scoring file. The "data" element contains a data frame with as many rows as variants that constitute the PGS score. The columns can vary. There are mandatory and optional columns. The mandatory columns are those that identify the variant, effect allele (effect_allele), and its respective weight (effect_weight) in the score. The columns that identify the variant can either be the rsID or the combination of chr_name and chr_position. The "data" element will be NULL is argument metadata_only is TRUE. For more information about the scoring file schema check vignette("pgs-scoring-file", package = "quincunx").

Examples

if (FALSE) {
# Read a PGS scoring file by PGS ID
# (internally, it translates the PGS ID
#  to the corresponding FTP URL)
try(read_scoring_file("PGS000655"))

# Equivalent to `read_scoring_file("PGS000655")`
url <- paste0(
  "http://ftp.ebi.ac.uk/",
  "pub/databases/spot/pgs/scores/",
  "PGS000655/ScoringFiles/",
  "PGS000655.txt.gz"
)
read_scoring_file(url)


# Reading from a local file
try(read_scoring_file("~/PGS000655.txt.gz"))
}