compareGC: Compare growth curves of tumor volume between Arms

In SCBIT-YYLab/DRAP: Drug Response Analysis Tailored for Drug Testing on Patient-Derived Tumor Models

Description

Compare the growth curves of tumor volume between pairwise arms with permuation test.

Usage

compareGC(data, compare.to = c('all','neg.control','pos.control'), 
          control, n = 1000, fun, adjust)

Arguments

data	a data frame of measured tumor volume data.
compare.to	the type of compare. "all" means comparing all pairs of arms, "neg.control" means comparing to negative control arm, "pos.control" means comparing to posative control arm.
control	the control arm. While compare to "neg.control", the negative control arm; While compare to "pos.control", the posative control arm.
n	the times of permuation.
fun	funciton used to caculate the statistics for permuation,MeanT or MeanW.
adjust	the method for adjust p.value.

Details

compareGC does pairwise comparisons of growth curves between all pairwise arms, or compared to negative/posative arm . p-values can be obtained with permutation test.

Value

compareGC returns a list with two components, stat and p.value, containing the observed statistics and the estimated p-value. compareGrowthCurves returns a data frame with components:

Arm1	name of first arm in a comparison;
Arm2	name of second arm in a comparison;
Stat	observed value of the statistic;
p.value	estimated p-value;
q.value	p-value adjusted for multiple testing.

References

Elso, C.M., et al. Leishmaniasis host response loci (lmr1-3) modify disease severity through a Th1/Th2-independent pathway. Genes and immunity 2004;5(2):93-100.

See Also

compareTwoGC

Examples

data(oneAN.volume.data)
## compare each pair of arms
compareGC(data = oneAN.volume.data, compare.to = 'all', n = 1000, 
          fun = MeanT, adjust = "BH")
compareGC(data = oneAN.volume.data, compare.to = 'all', n = 1000, 
          fun = MeanW, adjust = "BH")

## compare to negative control
compareGC(data = oneAN.volume.data, 
          compare.to = 'neg.control', control = 'Control', 
          n = 1000, fun = MeanT, adjust = "BH")

## compare to positive control
compareGC(data = oneAN.volume.data, 
          compare.to = 'pos.control', control = 'Treatment_1', 
          n = 1000, fun = MeanT, adjust = "BH")

  

SCBIT-YYLab/DRAP documentation built on April 7, 2020, 2:03 a.m.