| callFilter-methods {xps} | R Documentation |
Detection Call Filter.
The cutoff value defines the upper threshold for allowed detection call p-values. If e.g.
the number of samples exceeding this cutoff value is greater than samples then the
corresponding expression dataframe row is flagged, i.e. flag = 0.
The Detection Call Filter flags all rows with: flag = (sum(call[i] >= cutoff) >= samples)
Usage
callFilter(object)
callFilter(object, value)<-
object |
object of class PreFilter or UniFilter. |
value |
character vector c(cutoff, samples, condition). |
The method callFilter initializes the following parameters:
cutoff: | the cutoff value for the filter: | |
cutoff = 1.0: present/absent call is used. |
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cutoff < 1.0: detection p-value is used as cutoff. |
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samples: | this value depends on the condition used: |
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condition: | condition="samples": number of samples (default): |
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condition="percent": percent of samples. |
An initialized PreFilter or UniFilter object.
Christian Stratowa
## initialize PreFilter prefltr <- PreFilter() callFilter(prefltr) <- c(0.02,80.0,"percent") str(prefltr) ## initialize UniFilter unifltr <- UniFilter() callFilter(unifltr) <- c(0.02,80.0,"percent") str(unifltr)