Description Usage Arguments Value
saga_batch
removes batch effects from the joint data set. For each sample, the user must specify a batch number in the
"SAGA_USER_Samples.txt" file. If no batch numbers are available - you'll still have to provide a number for the samples. You can use
any integer number beginning with 1. The batch correction of the data set relies on the ComBat algorithm/package.
1 2 3 4 5 6 7 | saga_batch(
matrix.SAGA.qn,
matrix.test.qn,
rawdata,
pData.joint,
plotnumber = 2
)
|
matrix.SAGA.qn |
quantile normalized saga matrix |
matrix.test.qn |
quantile normalized test matrix |
rawdata |
SAGA raw data |
pData.joint |
matrix with combined SAGA data and user samples. |
plotnumber |
default=2 for PCA plot with samples in black; alternative: 1 for t-SNE plot |
eset.batch
batch corrected data set.
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