CalcSumstats {AllelicSeries} | R Documentation |
Generate summary statistics from individual-level data. Provide either a
list of data as generated by DGP
, or all of anno
, geno
,
and pheno
.
CalcSumstats(
anno = NULL,
covar = NULL,
data = NULL,
geno = NULL,
pheno = NULL,
is_binary = FALSE
)
anno |
(snps x 1) annotation vector. |
covar |
(subjects x covars) covariate matrix. |
data |
List of data containing the annotation vector |
geno |
(subjects x snps) genotype matrix. |
pheno |
(subjects x 1) phenotype vector. |
is_binary |
Is the phenotype binary? Default: FALSE. |
List containing the following items:
ld
: A SNP x SNP correlation (LD) matrix.
sumstats
: A SNP x 5 matrix of summary statistics, including the
. annotation, MAF, estimated effect size, standard error, and p-value.
type
: Either "binary" or "quantitative".'
data <- DGP()
sumstats <- CalcSumstats(data = data)