Usage
ComBat(expression_xls, sample_info_file, type = "txt", write = TRUE,
covariates = "all", par.prior = TRUE, filter = FALSE, skip = 0,
prior.plots = TRUE)
Arguments
expression_xls
A character string specifying gene expression file.
sample_info_file
A character string specifying sample file.
type
A character string specifying the type of the file, "txt" or "csv".
write
A Boolean variable indicating whether the output (adjusted data) should be written into a file.
covariates
A vector of integers or "all" if all covariates should be used. covariates=all will use all of the columns in your sample info file in the modeling (except array/sample name), if you only want use a some of the columns in your sample info file, specify these columns here as a vector (you must include the Batch column in this list).
par.prior
A Boolean character indicating whether the parametric adjustment should be applied.
filter
A Boolean variable indicating whether presence/absence call is used in the gene expression file.
skip
An integer value indicating the number of columns that contain the gene names. skip = 1 implies the first expression values start from column 2.
prior.plots
A Boolean variable indicating whether the prior plots should be given where black is a kernel density estimate of the batch effects. Quantile-quantile plots are also included. If the red and black lines do not match up well, use the nonparametric adjustment.