Description Usage Arguments Details Value Detailed explanation of the output contained in PIP and PNV Author(s) References See Also
Estimates sparse/shrunken coefficients (or loadings) of Logistic Factor Analysis (LFA).
Based on statistical sginificance of association between variables (i.e., SNPs) and logistic factors (LFs),
the conventional coefficients of LFs are shruken towards zeros, which improve its accuracy.
The only required inputs are the data matrix dat
and the number of LFs r
.
1 2 
dat 
a data matrix with 
p 

r 
a number (a positive integer) of significance logistic factors. 
s 
a number (a positive integer) of “synthetic” null variables (optional). 
B 
a number (a positive integer) of resampling iterations (optional). 
verbose 
a logical specifying to print the progress (default: TRUE). 
seed 
a seed for the random number generator (optional). 
save.all 
a logical specifying to save all objects, including a large SVD object (default: FALSE). 
By default, jaws.lfa
computes two canonical jackstraw weighted shrinkage estimators, namely PIP
and PNV
.
It is strongly advised that you take a careful look at your data and use appropriate graphical and statistical criteria
to determine r
(Note that r
does not include an intercept term).
If s
is not supplied, s
is set to about 10% of m
variables.
If B
is not supplied, B
is set to m*10/s
.
NOTE that you may input a m*r
matrix of pvalues obtained from running jackstraw.LFA
.
jaws.lfa
returns a list consisting of
p 
pvalues for association tests between variables and each of 
pi0 
proportion of variables not associated with 
PIP 
a list of outputs derived from the posterior inclusion probabilities method (including 
PNV 
a list of outputs derived from the proportion of null variables method (including 
PIP
and PNV
a matrix of posterior inclusion probabilities (equivalent to 1lfdr) for m
coefficients and r
LFs.
a vector of estimated proportion of null variables for r
LFs.
a m*r
matrix of shrunken coefficients.
a m*n
matrix of shrunken allele frequencies.
a vector of shrunken McFadden's pseudo R^2 measures for r
LFs.
Neo Chung [email protected]
Chung and Storey (2015) Forthcoming
jackstraw.LFA jaws.pca
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