propPowerSampleSize: Calculate sample size or power required in a 2-sample or...

In gmelloni/PrecisionTrialDesigner: A Tool to Analyze and Design NGS Based Custom Gene Panels

Calculate sample size or power required in a 2-sample or 1-sample proportion equality study

Description

This plot method returns a scatter plot of required sample size at screening by statistical power divided by couples of case-control probabilities.

Usage

propPowerSampleSize(object
, var=c(NA , "drug" , "group" , "gene_symbol" , "alteration_id" , "tumor_type")
, alterationType=c("copynumber" , "expression" , "mutations" , "fusions")
, tumor_type=NULL
, stratum=NULL
, tumor.weights=NULL
, tumor.freqs=NULL
, pCase=NULL
, pControl=NULL
, side = c(2,1)
, type=c("chisquare" , "arcsin" , "exact")
, alpha=0.05
, power=NULL
, sample.size=NULL
, case.fraction=0.5
, collapseMutationByGene=TRUE
, collapseByGene=FALSE
, round.result=TRUE
, priority.trial=NULL
, priority.trial.order=c("optimal" , "as.is")
, priority.trial.verbose=TRUE
, noPlot=FALSE)

Arguments

object	a CancerPanel object
var	one among NA , "drug" , "group" , "gene_symbol" , "alteration_id" or "tumor_type". It defines the arms of the studies to be projected. With var=NA, the projection of the entire panel is displayed.
alterationType	what kind of alteration to include. It can be one or more between "copynumber", "expression", "mutations", "fusions". Default is to include all kind of alterations.
tumor_type	only plot one or more tumor types among the ones available in the object.
stratum	a character vector containing one or more specific elements of var to be plotted instead of all the arms of the study. If it is not present, a warning is raised and the full design is returned.
tumor.weights	A named vector of integer values containing an amount of samples to be randomly sampled from the data. Each element should correspond to a different tumor type and is named after its tumor code. See details
tumor.freqs	A named vector of values between 0 and 1 which sum 1. It contains the expected proportion of patients that are planned to be screened. See Details
pCase	a numerical vector of one or more postulated proportions for cases (between 0 and 1)
pControl	a numerical vector of one or more postulated proportions for controls of the same length of pCase (between 0 and 1)
side	perform a 2-tail or 1-tail calculation. Default 2
type	calculate sample size using chisquare, arcsin or exact method. chisquare is used for a 2-sample equality while the other two are used in case in case pControl is fixed (1-sample case). case.fraction has no effect using arcsin or exact type.
alpha	a numerical value between 0 and 1 that reports the type I error threshold. Default 0.05 (5%)
power	a numerical vector of values between 0 and 1 that expresses the level of type II error. It is used to estimate sample size
sample.size	a positive integer numerical vector that reports the postulated sample size at screening. It is used to estimate the power of the study.
case.fraction	a numerical value between 0 and 1 representing the fraction of total sample size allocated to group 'Case'. Group control have an allocation of 1 - case.fraction
collapseMutationByGene	A logical that collapse all mutations on the same gene for a single patient as a single alteration.
collapseByGene	A logical that collapse all alterations on the same gene for a single patient as a single alteration. e.g. if a sample has TP53 both mutated and deleted as copynumber, it will count for one alteration only.
round.result	logical indicating if the sample size should be rounded with ceiling or not.
priority.trial	A character vector of drugs or group levels to start the design of a priority trial. See Details.
priority.trial.order	Either "optimal" or "as.is". If "optimal" is used, the screening starts from the rarest drug or group level up to the most common to guarantee minimal sample size at screening. In case of "as.is", the order of priority.trial remains unchanged.
priority.trial.verbose	If TRUE, the result of a priority.trial will be a complete report in a 5-element list.
noPlot	if TRUE, the plot is not shown and data are reported instead.

Details

This method estimates sample size or power on the basis of one of the two information. Using multiple sample sizes or power, power curves are reported simulating different scenarios. Power or sample size are required but not both at the same time. HR must be also set but if a vector is provided, the plot will show multiple curves according to the various hazard ratios. 'p.event', 'alpha' and 'case.fraction' are instead fixed for all the arms of the study (represented by the 'var' parameter).

If noPlot=TRUE, a data.frame with 6 column is reported instead:

Var

levels of chosen variable

ScreeningSampleSize

total sample size estimation at screening on the basis of frequency of alteration

EligibleSampleSize

sample size estimated as sum of cases and controls after screening

Beta

tested beta values

Power

tested 1 - beta values

Proportion.In.Case.Control

couples of pCase - pControl tested

The algorithm estimates sample size on the basis of no a priori probability of finding a case or control subject ("EligibleSampleSize" column). In a basket or umbrella design, this number must be multiplied by the frequency of alteration that we expect to find based on the simulation run on the panel. If our panel can cover the 50% of the samples with a target therapy and 100 samples are required to reach 80% power, we have to screen at least 200 patients in order to reach the desired number of cases in the sample size ("ScreeningSampleSize" column).

Similarly, if you want to estimate the power of the panel given an estimated sample size, we first multiply 'sample.size' by the frequency of expected alterations and then perform power estimation. 'sample.size' is therefore intended at screening.

When 'var' variable is set, the algorithm provides the estimated sample size for each stratum of the variable. For example, if we set it to 'drug', a power curve for each drug type is displayed, without taking into account possible overlaps. If a sample shows multiple targettable alterations, it will be reused for every drug type that targets those alterations.

By default, propPowerSampleSize will use all the available data from the object, using all the samples for the requested alterationTypes. Nevertheless, one could be interested in creating a compound design that is composed by a certain number of samples per tumor type. This is the typical situation of basket trials, where you seek for specific alteration, rather than specific tumor types and your design can be stopped when the desired sample size for a given tumor type is reached. By adding tumor.weights, we can achieve such target (see examples). Unfortunately, there are two main drawbacks in doing so:

1. small sample size: by selecting small random samples, the real frequency can be distorted. to avoid this, it is better to run several small samples and then bootstrap them

2. recycling: if the sample size for a tumor type requested by the user is above the available number of cBioportal samples, the samples are recycled. This has the effect of stabilizing the frequencies but y_measure = "absolute" will have no real meaning when the heterogeneity of the samples is lost.

A user balanced design can be also obtained using tumor.freqs parameter. In this case the fraction of altered samples are first calculated tumor-wise and then reaggregated using the weights provided by tumor.freqs. If the fraction of altered samples are 0.3 and 0.4 for breast cancer and lung cancer respectively, if you set tumor.freqs = c(brca=0.9 , luad=0.1), the full design will have a frequency equal to 0.3*0.9 + 0.4*0.1 = 0.31, that is basically equal to the one of breast samples. If this parameter is not set, the total amount of samples available is used with unpredictable balancing.

Both tumor.freqs and tumor.weights can achieve a balanced design according to user specification. To have a quick idea of the sample size required, it is better to use the former. To get an idea about the possible distribution of sample size giving a few samples (for example a minimum and a maximum sample size) it is better to run the function with tumor.weights several times and aggregate the results.

If priority.trial is set, a cascade design is build up. Given a set of parameter (power, pCase, pControl , alpha, etc.) an Eligible Sample Size (ESS) is calculated that is the same across drugs/groups. The total Screening Sample Size (SSS) is calculated following this scheme:

1. Start screening with the first drug/group, reaching the sample size necessary to reach ESS

2. From the samples not eligible for the first drug/group, test the second drug/group and collects as many samples as possible up to ESS

3. Continue using the samples not eligible to the end of all drugs/levels. Stop if there are no leftovers.

4. If all the drugs/groups have reached ESS, stop. Otherwise start a new screening with the first drug/group that has not reached ESS

5. Repeat from point 2 up to completion

If priority.trial.order is set, the user can decide if the drugs/group levels must follow a precise order (as.is) or if the screening can start from the rarest drug/group level up to the most common (optimal). Following the optimal priority trial guarantees the best possible allocation with the minimum screening.

Value

If noPlot = FALSE (default) a scatter plot is returned. If noPlot = TRUE, a data.frame is returned. In case priority.trial is set, a list of length-5-lists is reported. See vignette for details.

Author(s)

Giorgio Melloni, Alessandro Guida

References

Chow S, Shao J, Wang H. 2008. Sample Size Calculations in Clinical Research. 2nd Ed. Chapman & Hall/CRC Biostatistics Series. page 85/89

See Also

coveragePlot survPowerSampleSize

Examples

# Load example CancerPanel object
data(cpObj)
# Show the study design by tumor type:
# 3 pCase - pControl couples and 4 power levels
# The full design is weighted using tumor.freqs
# The final sample size is composed by 90% luad and 10% brca
propPowerSampleSize(cpObj 
  , var = "tumor_type"
  , pCase = c(0.7, 0.8 , 0.9)
  , pControl = rep(0.5 , 3) 
  , power=c(0.5 , 0.6 , 0.7 , 0.8 , 0.9)
  , tumor.freqs = c(brca=0.1 , luad=0.9))
# Return power levels giving sample sizes at screening
propPowerSampleSize(cpObj
  , var = NA 
  , pCase = c(0.7, 0.8 , 0.9)
  , pControl = rep(0.5 , 3) 
  , sample.size=c(100 , 300 , 500 , 1000) 
  , noPlot=FALSE)

gmelloni/PrecisionTrialDesigner documentation built on March 3, 2023, 6:10 a.m.