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