cqtest: Chen-Qin test statistic

In MethylCapSig: Detection of Differentially Methylated Regions using MethylCap-Seq Data

Description

Calculates the two sample Chen-Qin test statistic and p-value.

Usage

cqtest(X, Y)

Arguments

X	A matrix of dimension n \times k whose rows represent the samples collected from n (≥q 3) individuals from the first group on k variates.
Y	A matrix of dimension m \times k whose rows correspond to samples collected from m (≥q 3) individuals from the second group on k variates. Default value is null. If not specified, the function performs a one-sample test using X.

Details

The Chen-Qin test statistic is used to test equality of mean vectors for two groups of multivariate observations, where the dimension is greater than the sample size. cqtest takes matrices X and Y as arguments whose rows correspond to samples from the two groups respectively. Depending on the values in X and Y, the function initially determines whether to perform a one-sample test ( \mathop{∑}_{i,j} X_{ij}^2 = 0 or \mathop{∑}_{i,j} Y_{ij}^2 = 0) or a two-sample test. The appropriate test statistic is then calculated and is returned along with the p-value which is calculated using right-tailed normal distribution.

Note: The Chen-Qin test involves calculations on the data which require at least three samples in both the groups to evaluate the test statistic. See Chen and Qin (2010) for further details.

Value

A 2 \times 1 vector consisting of the test statistic and the p-value.

Author(s)

Deepak N. Ayyala, Javkhlan-Ochir Ganbat.

References

Chen, S. X. and Qin, Y. (2010) A two-sample test for high-dimensional data with applications in gene-set testing, Annals of Statistics, 38, 808 – 835.

Examples

data(diffMethylData)
cqtest(diffMethylData$region1.x, diffMethylData$region1.y)
# cqtest(diffMethylData$region2.x, diffMethylData$region2.y)

Example output

[1] -0.3323809  0.6301992

MethylCapSig documentation built on May 2, 2019, 9:24 a.m.