This code is associated with the paper
Pre-requisites
The following R packages are pre-requisites for running kinetx:
minpack
psych
kinetx dataset: 10 raw datafiles produced by the flow cytometry assay described in the above assay are included under 'data'. These allow the code to be tested.
Summary file format:
Format of functional data summary file:
donor - unique donor number taken from raw datafile directory name
output - function
measure - FL1 or FL4
agonist -
concentration -
drug -
0Secs - level at 10 seconds
10Secs - level at 10 seconds
20Secs - level at 20 seconds
30Secs - level at 30 seconds
40Secs - level at 40 seconds
60Secs - level at 60 seconds
90Secs - level at 90 seconds
120Secs - level at 120 seconds
180Secs - level at 180 seconds
10SecRoc - rate of change between 0 and 10 seconds
20SecRoc - rate of change between 10 and 20 seconds
30SecRoc - rate of change between 20 and 30 seconds
40SecRoc - rate of change between 30 and 40 seconds
60SecRoc - rate of change between 40 and 60 seconds
90SecRoc - rate of change between 60 and 90 seconds
120SecRoc - rate of change between 90 and 120 seconds
180SecRoc - rate of change between 120 and 180 seconds
IsotypeMedian - median level of isotype
zeroPoint - level at zero
maxRateChange -
maxRateChangePosition -
minRateChange -
minRateChangePosition -
maxRateAccel - maximum rate of acceleration
maxRateAccelPosition -
Label -
FL1: pred120 < 4000 low responder FL4: pred120 < 1000 low responder
LabelMetric: decreasing 0.9 < linear < 2 increasing
LabelMetric - Roc120/(Roc10 + Roc20)/2
RocLabel -
FL1 RoC: slow 40 < medium < 80 fast
FL4 RoC: slow 5 < medium < 10 fast
Roc - Rate of change between 0 and 120 seconds
EarlyRateLabel -
FL1: slow 40 < medium < 80 fast
FL4: slow 4 < medium < 12 fast
EarlyRateMetric - Rate of change in first 20 seconds
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