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. |
||
cutoff < 1.0 : detection p-value is used as cutoff. |
||
samples : | this value depends on the condition used: |
|
condition : | condition="samples" : number of samples (default): |
|
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)