ematAdjust | R Documentation |
Centers and scales gene expression matrix so that each row
has mean=0 and sd=1. If input data is non-normalized sequencing count
data, normalization should be performed by setting normMethod
. This
also enforces log2-transformation.
ematAdjust(
emat,
center = TRUE,
scale = TRUE,
signalFilt = 0,
verbose = getOption("verbose"),
...
)
emat |
a numeric matrix with row features and sample columns. |
center |
numeric of same length as |
scale |
numeric of same length as |
signalFilt |
numeric setting feature filtering. Specifically rows
where |
verbose |
logical, console messages output. |
... |
additional arguments passed to normalizeBetweenArrays and calcNormFactors depending normalization method selected. |
ematAdjust
performs row-wise scaling and centering by passing matrix
to scale
. Setting scale
and center
may be
useful for predicting new samples based on row-wise means and standard
deviations from prior (identically processed) datasets. If e.g.
signalFilt=.1
features with maximum below emat 10th
percentile are discarded.
A row-wise centered and scaled matrix. Output matrix will have fewer rows than input if signalFilt>0.
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