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Exclude rows with no variance from batch adjustment #13

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Exclude rows with no variance from batch adjustment #13

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17654c9
Added check for rows in input dat with no variance
khughitt May 28, 2016
ca185e0
Updated ComBat function to ignore genes with zero variance when adjus…
khughitt May 28, 2016
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20 changes: 20 additions & 0 deletions R/ComBat.R
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,19 @@
#'

ComBat <- function(dat, batch, mod=NULL, par.prior=TRUE,prior.plots=FALSE,mean.only=FALSE,ref.batch=NULL) {
# check for genes with uniform expression; if such genes exist, they will
# be temporarily removed from the data matrix before performing batch
# adjustment and add back in before returning the final result.
zero.var.rows <- apply(dat, 1, var) == 0

if (sum(zero.var.rows) > 0) {
cat(sprintf("Found %d genes with uniform expression; these will not be adjusted for batch.\n", sum(zero.var.rows)))

# keep a copy of the original data matrix and remove zero var rows
dat.orig <- dat
dat <- dat[!zero.var.rows,]
}

# make batch a factor and make a set of indicators for batch
if(mean.only==TRUE){cat("Using the 'mean only' version of ComBat\n")}
if(length(dim(batch))>1){stop("This version of ComBat only allows one batch variable")} ## to be updated soon!
Expand Down Expand Up @@ -212,6 +225,13 @@ ComBat <- function(dat, batch, mod=NULL, par.prior=TRUE,prior.plots=FALSE,mean.o
if(!is.null(ref.batch)){
bayesdata[, batches[[ref]]] <- dat[, batches[[ref]]]
}

# if genes genes with uniform expression were held out, add them back in now
if (sum(zero.var.rows) > 0) {
# keep a copy of the original data matrix and remove zero var rows
dat.orig[!zero.var.rows,] <- bayesdata
bayesdata <- dat.orig
}

return(bayesdata)

Expand Down