ppcca: Fitting PPCCA model

In syspremed/exploBATCH: Explore batch effect (exploBATCH) is a package for discovering and correcting for batch effect using an approach in Nyamundanda et al (2017).

Description

Fitting PPCCA model

Usage

ppcca(Y, Yc, tYc, X, S, sumdiS, muhat, tp, tmp, minq = 2, maxq = 3, eps = 0.8, n.cores)

Arguments

Y	Expression data
Yc	Centered and scaled data
tYc	Transposed centered and scaled data
X	Covariates
S	Sample covariance
sumdiS	Sum of the diagonal elements of sample covariance
muhat	Average expression of all features
tp	Number of dimensions from eigen
tmp	Eigen decomposion
minq	Minimum number of PCs considered
maxq	Maximum number of PCs considered
eps	Smallest value for convergence assessment
n.cores	Number of cores

Details

Fitting PPCCA model

Value

Fitting PPCCA model

Author(s)

Nyamundanda, G., Poudel, P., Patil, Y. and Sadanandam, A.

References

Nyamundanda, G., Poudel, P., Patil, Y. and Sadanandam, A., 2017. A novel and robust statistical method to diagnose and correct batch effects in genomic data.

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

syspremed/exploBATCH documentation built on May 23, 2019, 9:34 a.m.