adjLDStat {qgg} | R Documentation |
Check concordance between marker effect and sparse LD matrix.
Description
Check concordance between predicted and observed marker effect. Marker effect is predicted based on sparse LD matrix in Glist.
Usage
adjLDStat(
stat = NULL,
Glist = NULL,
chr = NULL,
region = NULL,
msize = NULL,
threshold = 1e-05,
overlap = NULL,
niter = 5
)
Arguments
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 |
[Package qgg version 1.1.6 Index]