getbetap.A: Momoent Corrected Correlation

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/getbetap.A.R

Description

Computes association statistics, the first four moments of the trend statistic A under permutation, and p-values based on the Beta density approximation.

Usage

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getbetap.A(getAmoment.list,A=NULL,fix.obs=F)

Arguments

getAmoment.list

A list which contains all the items generated by getAmoment function.

A

The vector A is composed of elements A_i=∑_j x_{ij} y_j. In other words, each A_i is the observed statistic of interest. getbetap.A also allows the user to input the A vector directly. This is useful mainly for debugging purposes, or for obtainting approximate p-values across a grid of hypothetical A values.

fix.obs

this option itentifies and improves the p-values using for MCC_1 features with implausibily small MCC p-values.

Details

mcc utilizes a general framework for testing the association between features and clinical variables. It simultaneously performs up to millions of tests by using simple parametric approximations applied to exact permutation moments.

Value

The function returns an object of class mcc.

Author(s)

Yi-Hui Zhou: [email protected]

References

Yi-Hui Zhou, Fred Wright, 2013, Fast And Robust Association Testing For High-Throughput Testing, Submitted.

See also the vignette included with this package.

See Also

getAmoment, getAkmoment, getbetap.A.2.

Examples

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set.seed(1)
m=300
n=30
x=matrix(rnorm(m*n),m,n)
y=c(rep(1,15),rep(2,15))
z=c(rep(1,25),rep(2,5))
output=getbetap.A(getAmoment(x,y,z),A=NULL,fix.obs=FALSE)
#names(output)
#[1] "twosidedp"    "rightp"       "leftp"        "pdouble"      "chebyshev.p" 
#[6] "pt"           "lowest.alpha"

mcc documentation built on May 30, 2017, 3:29 a.m.