modFilter imposes a hard filter for (gene expression) feature data.
modFilter(object, threshold, maximum, beta1, beta2, plotSkip = TRUE)# S4 method for ExprsArray
modFilter(object, threshold, maximum, beta1, beta2,
plotSkip = TRUE)
Specifies the ExprsArray object to undergo pre-processing.
A numeric scalar. The value below which to assign this value.
A numeric scalar. The value above which to assign this value.
A numeric scalar. The max - min range above which to
include the feature. Inclusive with beta2.
A numeric scalar. The max / min ratio above which to
include the feature. Inclusive with beta1.
A logical scalar. Toggles whether to produce side-by-side plots
of the before and after ExprsArray summary.
A pre-processed ExprsArray object.
ExprsArray: Method to filter an ExprsArray object.
This method reproduces the hard filter described by Deb and Reddy (2003)
for pre-processing the hallmark Golub ALL/AML dataset. This filter
first sets all values less than threshold to threshold
and all values greater than maximum to maximum.
Next, this method includes only those features with (a) a range greater
than beta1, and also (b) a ratio of maximum feature expression to
minimum feature expression greater than beta2.