filterCategory: Filter Ct values based on their feature categories.
In HTqPCR: Automated analysis of high-throughput qPCR data

Description Usage Arguments Value Author(s) See Also Examples

Ct values corresponding to selected feature categories will be replaced by NA. Generally, the feature categories indicate how reliable the values are.

1	filterCategory(q, na.categories = c("Unreliable", "Undetermined"))

`q`	a qPCRset object.
`na.categories`	character vector, with the name(s) of the feature categories where Ct values will be considered NA.

A qPCRset object like the input, but with the selected Ct values replaced by NAs

Heidi Dvinge

setCategory for adjusting the categories.

data(qPCRraw)
qPCRraw2 <- setCategory(qPCRraw, groups=NULL)
x <- filterCategory(qPCRraw2)
summary(qPCRraw)
summary(x)

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Categories after Ct.max and Ct.min filtering:
             sample1 sample2 sample3 sample4 sample5 sample6
OK               313     264     327     295     296     286
Undetermined      68     119      56      86      86      96
Unreliable         3       1       1       3       2       2
        sample1  sample2  sample3 sample4  sample5  sample6 
Min.    " 7.218" " 7.408" " 6.19" " 6.853" " 6.787" " 5.133"
1st Qu. "26.738" "28.855" "27.90" "26.964" "27.913" "27.514"
Median  "28.937" "30.994" "29.92" "29.943" "30.778" "29.931"
Mean    "29.543" "32.190" "30.35" "30.590" "30.995" "30.663"
3rd Qu. "33.323" "35.985" "32.98" "34.694" "34.702" "35.046"
Max.    "40.000" "40.000" "40.00" "40.000" "40.000" "40.000"
        sample1 sample2 sample3 sample4 sample5 sample6
Min.    "11.28" "11.57" "10.62" "11.49" "10.46" "10.46"
1st Qu. "25.97" "27.92" "26.99" "26.81" "26.97" "26.83"
Median  "27.94" "29.48" "28.98" "28.45" "28.96" "27.98"
Mean    "27.88" "29.32" "29.12" "28.51" "28.95" "28.36"
3rd Qu. "29.97" "31.91" "30.97" "30.97" "31.64" "30.95"
Max.    "35.00" "35.00" "34.99" "34.92" "34.97" "34.99"
NA's    "74"    "120"   "62"    "84"    "88"    "90"