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-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/AllGenerics.R, R/deSet-methods.R

-\docType{methods}

-\name{apply_jackstraw}

-\alias{apply_jackstraw}

-\alias{apply_jackstraw,deSet-method}

-\title{Non-Parametric Jackstraw for Principal Component Analysis (PCA)}

-\usage{

-apply_jackstraw(object, r1 = NULL, r = NULL, s = NULL, B = NULL,

-  covariate = NULL, verbose = TRUE, seed = NULL)

-

-\S4method{apply_jackstraw}{deSet}(object, r1 = NULL, r = NULL, s = NULL,

-  B = NULL, covariate = NULL, verbose = TRUE, seed = NULL)

-}

-\arguments{

-\item{object}{\code{S4 object}: \code{\linkS4class{deSet}}}

-

-\item{r1}{a numeric vector of principal components of interest. Choose a subset of r significant PCs to be used.}

-

-\item{r}{a number (a positive integer) of significant principal components.}

-

-\item{s}{a number (a positive integer) of synthetic null variables. Out of m variables, s variables are independently permuted.}

-

-\item{B}{a number (a positive integer) of resampling iterations. There will be a total of s*B null statistics.}

-

-\item{covariate}{a data matrix of covariates with corresponding n observations.}

-

-\item{verbose}{a logical indicator as to whether to print the progress.}

-

-\item{seed}{a seed for the random number generator.}

-}

-\value{

-\code{apply_jackstraw} returns a \code{list} containing the following

-slots:

-\itemize{

-\item{\code{p.value} the m p-values of association tests between variables

-and their principal components}

-\item{\code{obs.stat} the observed F-test statistics}

-\item{\code{null.stat} the s*B null F-test statistics}

-}

-}

-\description{

-Estimates statistical significance of association between variables and

-their principal components (PCs).

-}

-\details{

-This function computes m p-values of linear association between m variables

-and their PCs. Its resampling strategy accounts for the over-fitting

-characteristics due to direct computation of PCs from the observed data

-and protects against an anti-conservative bias.

-

-Provide the \code{\linkS4class{deSet}},

-with m variables as rows and n observations as columns. Given that there are

-r significant PCs, this function tests for linear association between m

-varibles and their r PCs.

-

-You could specify a subset of significant PCs

-that you are interested in r1. If PC is given, then this function computes

-statistical significance of association between m variables and PC, while

-adjusting for other PCs (i.e., significant PCs that are not your interest).

-For example, if you want to identify variables associated with 1st and 2nd

-PCs, when your data contains three significant PCs, set r=3 and r1=c(1,2). 

-

-Please take a careful look at your data and use appropriate graphical and

-statistical criteria to determine a number of significant PCs, r. The number

-of significant PCs depends on the data structure and the context. In a case

-when you fail to specify r, it will be estimated from a permutation test

-(Buja and Eyuboglu, 1992) using a function \code{\link{permutationPA}}.

-

-If s is not supplied, s is set to about 10% of m variables. If B is not

-supplied, B is set to m*10/s.

-}

-\examples{

-library(splines)

-data(kidney)

-age <- kidney$age

-sex <- kidney$sex

-kidexpr <- kidney$kidexpr

-cov <- data.frame(sex = sex, age = age)

-# create models

-null_model <- ~sex

-full_model <- ~sex + ns(age, df = 4)

-# create deSet object from data

-de_obj <- build_models(data = kidexpr, cov = cov, null.model = null_model,

-                      full.model = full_model)

-## apply the jackstraw

-out = apply_jackstraw(de_obj, r1=1, r=1)

-## Use optional arguments

-## For example, set s and B for a balance between speed of the algorithm and accuracy of p-values

-## out = apply_jackstraw(dat, r1=1, r=1, s=10, B=1000, seed=5678)

-

-}

-\author{

-Neo Christopher Chung \email{nc@princeton.edu}

-}

-\references{

-Chung and Storey (2013) Statistical Significance of

-Variables Driving Systematic Variation in

-High-Dimensional Data. arXiv:1308.6013 [stat.ME]

-\url{http://arxiv.org/abs/1308.6013}

-

-More information available at \url{http://ncc.name/}

-}

-\seealso{

-\code{\link{permutationPA}}

-}

-