Description Usage Arguments Details Value Author(s) See Also Examples
Classify droplets as "NN", "NP", "PN" or "PP" depending on whether they lie above or below given thresholds. This is illustrated in the details and parameters for more detail.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | thresholdClassify(droplets, ch1Threshold = 6500, ch2Threshold = 2900, ...)
## S4 method for signature 'data.frame'
thresholdClassify(
droplets,
ch1Threshold = 6500,
ch2Threshold = 2900,
fullTable = TRUE
)
## S4 method for signature 'ddpcrWell'
thresholdClassify(
droplets,
ch1Threshold = 6500,
ch2Threshold = 2900,
classMethodLabel = "thresholds"
)
## S4 method for signature 'ddpcrPlate'
thresholdClassify(
droplets,
ch1Threshold = 6500,
ch2Threshold = 2900,
classMethodLabel = "thresholds"
)
|
droplets |
A |
ch1Threshold |
The channel 1 upper bound for the NN and NP classes. Defaults to 8000 |
ch2Threshold |
The channel 2 upper bound for the NN and PN classes. Defaults to 3000. |
... |
Other options depending on the type of |
fullTable |
Whether to return a data frame including amplitude figures.
If |
classMethodLabel |
A name (as a character string) of the classification method. Defaults to "thresholds". |
The threshold
parameters correspond to those in the
following diagram:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | Ch1 ^ |
| |
| |
| PN | PP
| |
| |
a|__________|__________
| |
| |
| NN | NP
| |
| |
--------------------->
b Ch2
|
Specifically:
ch1Threshold
,
ch2Threshold
.
If droplets
is a data frame, return a data frame or factor
(depending on the trainingData
and fullTable
parameters) with
a classification for droplets in the chosen regions.
If droplets
is a ddpcrWell
object, return
a ddpcrWell
object with the appropriate classification.
If droplets
is a ddpcrPlate
object, return
a ddpcrPlate
object with the appropriate classification.
Anthony Chiu, anthony.chiu@cruk.manchester.ac.uk
This function is a special case of gridClassify
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ## Use thresholds to set a classification for a data frame.
gCl <- thresholdClassify(KRASdata[["E03"]],
ch1Threshold=6789, ch2Threshold=3000)
str(gCl)
## The same works for ddpcrWell objects.
aWell <- ddpcrWell(well=KRASdata[["E03"]])
aWell <- thresholdClassify(aWell, ch1Threshold=6789, ch2Threshold=3000)
str(aWell)
## ddpcrPlate objects work in exactly the same way.
krasPlate <- ddpcrPlate(wells=KRASdata)
krasPlate <- thresholdClassify(krasPlate,
ch1Threshold=6789, ch2Threshold=3000)
lapply(plateClassification(krasPlate, withAmplitudes=TRUE), head, n=1)
## The default classification method (column name) is 'threshold'. It can be
## changed by providing a label.
krasPlate <- ddpcrPlate(wells=KRASdata)
krasPlate <- thresholdClassify(krasPlate,
ch1Threshold=6789, ch2Threshold=3000,
classMethodLabel="manual")
lapply(plateClassification(krasPlate, withAmplitudes=TRUE), head, n=1)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.