| gapFilter-methods {xps} | R Documentation |
This method initializes the Gap Filter.
The gapFilter looks for genes that might usefully discriminate between two groups.
To do this we look for a gap in the ordered expression values. The gap should come in the
central portion, thus a parameter window is defined to exclude jumps in the initial
window values and the final window values.
The Gap Filter flags all rows with: flag = ((gap[i+1] - gap[i])/mean >= cutoff)
gapFilter(object)
gapFilter(object, value)<-
object |
object of class PreFilter. |
value |
numeric vector c(cutoff, window, trim, epsilon). |
The method gapFilter initializes the following parameters:
cutoff: | the cutoff level for the filter. | |
window: | trim value for the ordered expression levels (default is window=0.05). |
|
trim: | the trim value for trimmed mean (default is trim=0). |
|
epsilon: | value to replace mean (default is epsilon=0.01): |
|
epsilon > 0: replace mean=0 with epsilon. |
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epsilon = 0: always set mean=1. |
Note, that for epsilon = 0 the filter flags all rows with: (gap[i+1] - gap[i]) >= cutoff
An initialized PreFilter object.
Christian Stratowa
prefltr <- PreFilter() gapFilter(prefltr) <- c(0.3,0.05,0.0,0.01) str(prefltr)