DMLtest.multiFactor {DSS} | R Documentation

## Perform statistical test for BS-seq data from general experimental design

### Description

This function takes the linar model fitting results and performs Wald test at each CpG site, then return test statistics, p-values and FDR.

### Usage

    DMLtest.multiFactor(DMLfit, coef = 2, term, Contrast)

### Arguments

`DMLfit` | Result object returned from 'DMLfit.multiFactor' function.
`coef` | It can be an integer to indicate which coefficient in the linear model is be tested for being zero. Be careful of intercept. If the model contains intercept, coef=2 indicate testing the first factor in the formula. If the model has no intercept, testing first factor should use coef=1. It can also be a character for the terms to be tested. In that case it must match one of the column names in the design matrix. One can look at colnames(DMLfit$X) to obtain the column names.
`term` | The term(s) to be tested, as one or a vector of characters. Can be multiple terms. See 'Hypothesis test' section for details.
`Contrast` | A contrast matrix for hypothesis testing. The number of rows must equal to the number of columns in the design matrix ncol(DMLfit$X). See 'Hypothesis test' section for details.

### Value

A data frame with following columns: chr, pos, stat, pvals, fdr. Each row is for a CpG site. Note that the CpG sites are sorted by chromosome and position.

### Hypothesis test

User can specify one of the following parameter for testing: 'coef', 'term', or 'Contrast'.

When specifying 'coef', it tests *one* parameter in the model, which corresponds to one column in the design matrix. In this case, A Wald test is performed using the estimated coefficient and standard error from 'DMLfit.multiFactor'. P-values are derived from test statistics based on normal distribution.

When specifying 'term', it tests the whole term in the model. If the term is continuous or a categorical variable with only two levels (one degree of freedom), it is equivalent to specifying 'coef' because it tests only one parameter in the model. However, when the term is a categorical variable with more than two levels, it will test multiple parameters at the same time so it's a compound hypothesis test, and a F-test will be performed.

Specifying 'Contrast' matrix provides the most flexible test procedure. It can test any linear combination of the parameter, and F-test will be performed. Let L be the contrast matrix. The hypothesis test performed is H0: L^T * beta = 0. Thus the number of rows in L must equal to the number of items of beta (which is the number of columns in the design matrix).

Using 'term' or 'Contrast' will be slower especially when there are a lot of CpG sites, because the computation cannot be vectorized (each CpG site has a different variance/covariance matrix for the estimated coefficients).

FDR is computed using cannonical Benjamini-Hochberg procedure.

### Author(s)

Hao Wu<hao.wu@emory.edu>

### See Also

DMLfit.multiFactor, DMLtest

### Examples

    ## Not run:
    data(RRBS)
    ## model fitting
    DMLfit = DMLfit.multiFactor(RRBS, design, ~case+cell+case:cell)

    ## hypothesis testing - following two lines do the same thing
    DMLtest.cell = DMLtest.multiFactor(DMLfit, coef=3)
    DMLtest.cell = DMLtest.multiFactor(DMLfit, coef="cellrN")

    ## this doesn't work
    DMLtest.cell = DMLtest.multiFactor(DMLfit, coef="cell")

    ## look at distributions of test statistics and p-values
    par(mfrow=c(1,2))
    hist(DMLtest.cell$stat, 100, main="test statistics")
    hist(DMLtest.cell$pvals, 100, main="P values")

    ## Using term or Contrast
    DMLfit = DMLfit.multiFactor(RRBS, design, ~case+cell)

    ## following 4 tests should produce the same results,
    ## since 'case' only has two levels.
    ## However the p-values from F-tests (using term or Contrast) are
    ## slightly different, due to normal approximation in Wald test.
    test1 = DMLtest.multiFactor(DMLfit, coef=2)
    test2 = DMLtest.multiFactor(DMLfit, coef="caseSLE")
    test3 = DMLtest.multiFactor(DMLfit, term="case")
    Contrast = matrix(c(0,1,0), ncol=1)
    test4 = DMLtest.multiFactor(DMLfit, Contrast=Contrast)
    cor(cbind(test1$pval, test2$pval, test3$pval, test4$pval))

    ## note the different usage of term and coef.
    ## 'term' has to be in the formula, whereas 'coef' has to be in colnames
    ## of the design matrix.
    DMLfit = DMLfit.multiFactor(RRBS, design, ~case+cell+case:cell)
    DMLtest.cell = DMLtest.multiFactor(DMLfit, coef="cellrN")
    DMLtest.cell = DMLtest.multiFactor(DMLfit, term="cell")
    DMLtest.int = DMLtest.multiFactor(DMLfit, coef="caseSLE:cellrN")
    DMLtest.int = DMLtest.multiFactor(DMLfit, term="case:cell")

    ## End(Not run)

[Package DSS version 2.34.0 Index]