pgs_get: Read in and sort PGS data

In LCBC-UiO/MOAS: MOAS convenience functions

Read in and sort PGS data

Description

Given the path containing PGS data, this function will read in PGS data for the PGS's specified and the significance levels provided. In order to correctly only keep rows of data from verified sources, the genetic_match_file is necessary to provide for a check.

Usage

pgs_get(
  pgs = c("AD", "AD_Jansen"),
  s_levels = c("S1", "S7", "S11"),
  pgs_path = character(),
  genetic_match_file = character(),
  include_cnt = FALSE,
  include_pheno = FALSE,
  include_genetic_debug = FALSE
)

Arguments

pgs	character vector of the PGS wanted
s_levels	character vector of the significance levels wanted
pgs_path	path to the directory where the PGS's are stored
genetic_match_file	path to the file containing the MOAS-genetics matching and debugging information
include_cnt	logical, whether to keep SNP count information
include_pheno	logical, whether to keep PHENO information
include_genetic_debug	logical, whether to keep all columns in the genetic_match_file in the final output

Value

a tibble / data.frame

See Also

Other pgs-functions: pgs_add_all(), pgs_add_single(), pgs_add(), pgs_get_all(), pgs_get_single(), pgs_read()

Examples

## Not run: 

pgs_get( pgs = "JansenAD",
         s_levels = c("S1", "S7", "S11"),
         pgs_path = "path/to/PGS_wAPOE/",
         genetic_match_file = character(),
)

# You can also toggle adding the CNT columns from the PGS, by changing
# include_cnt to TRUE
pgs_get( pgs = character(),
         s_levels = c("S1", "S7", "S11"),
         pgs_path = "path/to/PGS_wAPOE/",
         genetic_match_file = "path/to/gID_MOAS_match.tsv",
         include_cnt = FALSE
)


## End(Not run)

LCBC-UiO/MOAS documentation built on Aug. 28, 2023, 3:29 a.m.