GWAS.Rd
A GWAS object is a container for vectors of GWAS data, a correlation matrix, and meta-data regarding quality control procedures applied at the point of object creation / data import.
GWAS(
dat,
map = "default",
drop = FALSE,
fill = FALSE,
fill_rsid = FALSE,
missing_rsid = "fill_CHR:BP",
parallel_cores = parallel::detectCores(),
dbsnp_dir = genepi.utils::which_dbsnp_directory(),
filters = list(beta_invalid = "!is.infinite(beta) & abs(beta) < 20", eaf_invalid =
"eaf > 0 & eaf < 1", p_invalid = "!is.infinite(p)", se_invalid = "!is.infinite(se)",
alleles_invalid = "!is.na(ea) & !is.na(oa)", chr_missing = "!is.na(chr)", bp_missing
= "!is.na(bp)", beta_missing = "!is.na(beta)", se_missing = "!is.na(se)", p_missing =
"!is.na(p)", eaf_missing = "!is.na(eaf)"),
reference = NULL,
ref_map = NULL,
verbose = TRUE,
...
)
a valid string file path to be read by data.table::fread
or a data.table::data.table
object; the GWAS data source
a valid input to the ColumnMap
class constructor (a predefined map string id, a named list or character vector, or a ColumMap object)
a logical, whether to drop data source columns not in the column map
a logical, whether to add (NAs) missing columns present in the column map
but not present in the data source
either FALSE or a valid argument for the chrpos_to_rsid build
argument, e.g. "b37_dbsnp156"
a string, how to handle missing rsids: one of "fill_CHR:BP", "fill_CHR:BP_OA_EA", "overwrite_CHR:BP", "overwrite_CHR:BP:OA:EA", "none", or "leave"
an integer, number of cores to used for RSID mapping, default is maximum machine cores
path to the dbsnp directory of fst files see chrpos_to_rsid dbsnp_dir
argument
a list of named strings, each to be evaluated as an expression to filter the data during the quality control steps (above)
a valid string file path to be read by data.table::fread
or a data.table::data.table
object; the reference data
a valid input to the ColumnMap
class constructor (a predefined map id (a string), a named list or character vector, or a
ColumMap object) defining at least columns rsid
(or chr
, bp
), ea
, oa
and eaf
.
a logical, whether to print details
variable capture to be passed to the constructor, e.g. individual vectors for the slots, rather that dat
an S7 class genepi.utils::GWAS object
rsid
character, variant ID - usually in rs12345 format, however this can be changed with the missing_rsid
argument
chr
character, chromosome identifier
bp
integer, base position
ea
character, effect allele
oa
character, other allele
eaf
numeric, effect allele frequency
beta
numeric, effect size
se
numeric, effect size standard error
p
numeric, p-value
n
integer, total number of samples
ncase
integer, number of cases
strand
character, the strand + or -
imputed
logical, whether imputed
info
numeric, the info score
q
numeric, the Q statistic for meta analysis results
q_p
numeric, the Q statistic P-value
i2
numeric, the I2 statistic
trait
character, the GWAS trait
id
character, the GWAS identifier
source
character, data source; either the file path, or "data.table" if loaded directly
correlation
matrix, a correlation matrix of signed R values between variants
map
ColumnMap
, a mapping of class ColumnMap
qc
list, a named list of filters; name is the filter expression and value is an integer vector of rows that fail the filter