emQ: EM algorithm for PPCA model.

Description Usage Arguments Details Value Author(s) References Examples

View source: R/emQ.R

Description

EM algorithm for PPCA model.

Usage

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emQ(q, Yc, tYc, S, tmp, tp, p, Ip, Np, Nvp, C2p, picon, IQ, penalty, eps, repV, V)

Arguments

q

Number of PCs

Yc

Centered and scaled data

tYc

Transposed centered and scaled data

S

Sample covariance

tmp

Eigen decomposion

tp

Number of dimensions from eigen

p

Number of features

Ip

Identity matrix of p by p

Np

Some constant; n by p

Nvp

Some constant n by v by p

C2p

Some constant for the prior of the error variance

picon

Some constant for normal density computation

IQ

Identity matrices for different q values

penalty

penalty term for BIC

eps

Smallest value for convergence assessment

repV

Vector for maximum number of EM iteration in a vector

V

Maximum number of EM iterations.

Details

EM algorithm for PPCA model.

Value

EM algorithm for PPCA 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

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

gnyamundanda/exploBATCH documentation built on May 20, 2019, 3:31 p.m.