correctBatch: Batch correction approach based on the PPCCA model.

Description Usage Arguments Details Value Author(s) References Examples

View source: R/correctBatch.R

Description

Batch effect is corrected by subtracting its effect only in the affected dimensions or PCs. Both the corrected and uncorrected dimensions are then used to predict the data.

Usage

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correctBatch(res11, designX, Ys, batchCL, grps, conF, nt, cGsub, comres)

Arguments

res11

Results of fitting the PPCCA model.

designX

Design matrix for the covariates

Ys

Expression data

batchCL

A vector identifying batches.

grps

Number of batches

conF

A vector identifying biological classes.

nt

Number of biological classes

cGsub

Colors

comres

Results of ComBat correction

Details

Batch effect is corrected by subtracting its effect only in the affected dimensions or PCs. Both the corrected and uncorrected dimensions are then used to predict the data.

Value

Results in correctBatch folder in the working directory.

Author(s)

Gift Nyamundanda and Anguraj Sadanandam

References

Nyamundanda, G. and Sadanandam, A., 2016. A novel and robust statistical method to diagnose and correct batch effects in large-scale 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.

syspremed/exploBATCH documentation built on April 4, 2018, 6:54 a.m.