View source: R/genomic_statistics.R
adjLDStat | R Documentation |
Check concordance between predicted and observed marker effect. Marker effect is predicted based on sparse LD matrix in Glist.
adjLDStat(
stat = NULL,
Glist = NULL,
chr = NULL,
region = NULL,
msize = NULL,
threshold = 1e-05,
overlap = NULL,
niter = 5
)
stat |
data frame with marker summary statistics (see required format above) |
Glist |
list of information about genotype matrix stored on disk |
chr |
chromosome for which marker effect is checked |
region |
genome region (in base pairs) for which marker effect is checked |
msize |
is the number of markers used in the prediction |
threshold |
p-value threshold used for chisquare test for difference between observed and predicted marker effects |
overlap |
is the number of markers overlapping between adjacent genome region |
niter |
is the number of iteration used for detecting outliers |
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