MTP-class {multtest}R Documentation

Class "MTP", classes and methods for multiple testing procedure output

Description

An object of class MTP is the output of a particular multiple testing procedure, for example, generated by the MTP function. It has slots for the various data used to make multiple testing decisions, such as adjusted p-values and confidence regions.

Objects from the Class

Objects can be created by calls of the form
new('MTP',
statistic = ...., object of class numeric
estimate = ...., object of class numeric
sampsize = ...., object of class numeric
rawp = ...., object of class numeric
adjp = ...., object of class numeric
conf.reg = ...., object of class array
cutoff = ...., object of class matrix
reject = ...., object of class matrix
nulldist = ...., object of class matrix
call = ...., object of class call
seed = ...., object of class integer
)

Slots

statistic:
Object of class numeric, observed test statistics for each hypothesis, specified by the values of the MTP arguments test, robust, standardize, and psi0.
estimate:
For the test of single-parameter null hypotheses using t-statistics (i.e., not the F-tests), the numeric vector of estimated parameters corresponding to each hypothesis, e.g. means, differences in means, regression parameters.
sampsize:
Object of class numeric, number of columns (i.e. observations) in the input data set.
rawp:
Object of class numeric, unadjusted, marginal p-values for each hypothesis.
adjp:
Object of class numeric, adjusted (for multiple testing) p-values for each hypothesis (computed only if the get.adjp argument is TRUE).
conf.reg:
For the test of single-parameter null hypotheses using t-statistics (i.e., not the F-tests), the numeric array of lower and upper simultaneous confidence limits for the parameter vector, for each value of the nominal Type I error rate alpha (computed only if the get.cr argument is TRUE).
cutoff:
The numeric matrix of cut-offs for the vector of test statistics for each value of the nominal Type I error rate alpha (computed only if the get.cutoff argument is TRUE).
reject:
Object of class matrix, rejection indicators (TRUE for a rejected null hypothesis), for each value of the nominal Type I error rate alpha.
nulldist:
The numeric matrix for the estimated test statistics null distribution (returned only if keep.nulldist=TRUE; option not currently available for permutation null distribution, i.e., nulldist="perm"). By default (i.e., for nulldist="boot"), the entries of nulldist are the null value shifted and scaled bootstrap test statistics, with one null test statistic value for each hypothesis (rows) and bootstrap iteration (columns).
call:
Object of class call, the call to the MTP function.
seed:
An integer for specifying the state of the random number generator used to create the resampled datasets. The seed can be reused for reproducibility in a repeat call to MTP. This argument is currently used only for the bootstrap null distribution (i.e., for nulldist="boot"). See ? set.seed for details.

Methods

signature(x = "MTP")

[
: Subsetting method for MTP class, which operates selectively on each slot of an MTP instance to retain only the data related to the specified hypotheses.
as.list
: Converts an object of class MTP to an object of class list, with an entry for each slot.
plot
: plot methods for MTP class, produces the following graphical summaries of the results of a MTP. The type of display may be specified via the which argument.

1. Scatterplot of number of rejected hypotheses vs. nominal Type I error rate.

2. Plot of ordered adjusted p-values; can be viewed as a plot of Type I error rate vs. number of rejected hypotheses.

3. Scatterplot of adjusted p-values vs. test statistics (also known as "volcano plot").

4. Plot of unordered adjusted p-values.

5. Plot of confidence regions for user-specified parameters, by default the 10 parameters corresponding to the smallest adjusted p-values (argument top).

6. Plot of test statistics and corresponding cut-offs (for each value of alpha) for user-specified hypotheses, by default the 10 hypotheses corresponding to the smallest adjusted p-values (argument top).

The argument logscale (by default equal to FALSE) allows one to use the negative decimal logarithms of the adjusted p-values in the second, third, and fourth graphical displays. The arguments caption and sub.caption allow one to change the titles and subtitles for each of the plots (default subtitle is the MTP function call). Note that some of these plots are implemented in the older function mt.plot.

print
: print method for MTP class, returns a description of an object of class MTP, including sample size, number of tested hypotheses, type of test performed (value of argument test), Type I error rate (value of argument typeone), nominal level of the test (value of argument alpha), name of the MTP (value of argument method), call to the function MTP.

In addition, this method produces a table with the class, mode, length, and dimension of each slot of the MTP instance.

summary
: summary method for MTP class, provides numerical summaries of the results of a MTP and returns a list with the following three components.

1. rejections: A data.frame with the number(s) of rejected hypotheses for the nominal Type I error rate(s) specified by the alpha argument of the function MTP. (NULL values are returned if all three arguments get.cr, get.cutoff, and get.adjp are FALSE).

2. index: A numeric vector of indices for ordering the hypotheses according to first adjp, then rawp, and finally the absolute value of statistic (not printed in the summary).

3. summaries: When applicable (i.e., when the corresponding quantities are returned by MTP), a table with six number summaries of the distributions of the adjusted p-values, unadjusted p-values, test statistics, and parameter estimates.

update
: update method for MTP class, provides a mechanism to re-run the MTP with different choices of the following arguments - alternative, typeone, k, q, fdr.method, alpha, smooth.null, method, get.cr, get.cutoff, get.adjp, keep.nulldist. When evaluate is 'TRUE', a new object of class MTP is returned. Else, the updated call is returned. The MTP object passed to the update method must have a non-empty nulldist slot (ie: must have been called with 'keep.nulldist=TRUE').

Author(s)

Katherine S. Pollard, http://lowelab.ucsc.edu/katie/
with design contributions from Sandrine Dudoit and Mark J. van der Laan.

References

M.J. van der Laan, S. Dudoit, K.S. Pollard (2004), Augmentation Procedures for Control of the Generalized Family-Wise Error Rate and Tail Probabilities for the Proportion of False Positives, Statistical Applications in Genetics and Molecular Biology, 3(1). http://www.bepress.com/sagmb/vol3/iss1/art15/

M.J. van der Laan, S. Dudoit, K.S. Pollard (2004), Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate, Statistical Applications in Genetics and Molecular Biology, 3(1). http://www.bepress.com/sagmb/vol3/iss1/art14/

S. Dudoit, M.J. van der Laan, K.S. Pollard (2004), Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates, Statistical Applications in Genetics and Molecular Biology, 3(1). http://www.bepress.com/sagmb/vol3/iss1/art13/

Katherine S. Pollard and Mark J. van der Laan, "Resampling-based Multiple Testing: Asymptotic Control of Type I Error and Applications to Gene Expression Data" (June 24, 2003). U.C. Berkeley Division of Biostatistics Working Paper Series. Working Paper 121. http://www.bepress.com/ucbbiostat/paper121

See Also

MTP, MTP-methods, [-methods, as.list-methods, print-methods, plot-methods, summary-methods

Examples

## See MTP function: ? MTP

[Package multtest version 1.8.0 Index]