Description Usage Arguments Value References
View source: R/pCorShrinkData2.R
This function performs adaptive shrinkage of a matrix of
partial correlations using a similar model as CorShrinkMatrix
, but
with the option of being aided by bagging on the data matrix.
1 2 3 
data 
The samples by features data matrix. May contain NA values. 
type 
The type of bagging method used, if at all, for estimating the
partial corelation matrix. The three possible types are 

nbags 
If 
nboot 
The number of bootstrap samples used to compute the bootstrap
standard errors of the partial correlations used for shrinking
in 
thresh_up 
Upper threshold for correlations in 
thresh_down 
Lower threshold for correlations in 
tol 
The tolerance chosen to check how far apart the CorShrink matrix is from the nearest positive definite matrix before applying PD completion. 
report_model 
if TRUE, outputs the full adaptive shrinkage output, else outputs the shrunken vector. Defaults to FALSE. 
ash.control 
The control parameters for adaptive shrinkage 
If report_model = FALSE
, returns the adaptively shrunk
partial correlation matrix. If report_model = TRUE
, then the
function also returns all the details of the adaptive shrinkage model
output.
False Discovery Rates: A New Deal. Matthew Stephens bioRxiv 038216; doi: http://dx.doi.org/10.1101/038216
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