roast.DGEList {edgeR} | R Documentation

## Self-contained Gene Set Tests for Digital Gene Expression Data

### Description

Rotation gene set testing for Negative Binomial generalized linear models.

### Usage

    ## S3 method for class 'DGEList'
    fry(y, index = NULL, design = NULL, contrast = ncol(design), geneid = NULL,
          sort = "directional", ...)

    ## S3 method for class 'DGEList'
    roast(y, index = NULL, design = NULL, contrast = ncol(design), geneid = NULL,
          set.statistic = "mean", gene.weights = NULL, nrot = 1999, ...)

    ## S3 method for class 'DGEList'
    mroast(y, index = NULL, design = NULL, contrast = ncol(design), geneid = NULL,
           set.statistic = "mean", gene.weights = NULL, nrot = 1999,
           adjust.method = "BH", midp = TRUE, sort = "directional", ...)

### Arguments

`y` | `DGEList` object.
`index` | index vector specifying which rows (probes) of `y` are in the test set. Can be a vector of integer indices, or a logical vector of length `nrow(y)`, or a vector of gene IDs corresponding to entries in `geneid`. Alternatively it can be a data.frame with the first column containing the index vector and the second column containing directional gene weights. For `mroast` or `fry`, `index` is a list of index vectors or a list of data.frames.
`design` | the design matrix. Defaults to `y$design` or, failing that, to `model.matrix(~y$samples$group)`.
`contrast` | contrast for which the test is required. Can be an integer specifying a column of `design`, or the name of a column of `design`, or a numeric contrast vector of length equal to the number of columns of `design`.
`geneid` | gene identifiers corresponding to the rows of `y`. Can be either a vector of length `nrow(y)` or the name of the column of `y$genes` containing the gene identifiers. Defaults to `rownames(y)`.
`set.statistic` | summary set statistic. Possibilities are `"mean"`,`"floormean"`,`"mean50"` or `"msq"`.
`gene.weights` | numeric vector of directional (positive or negative) genewise weights. For `mroast` or `fry`, this vector must have length equal to `nrow(y)`. For `roast`, can be of length `nrow(y)` or of length equal to the number of genes in the test set.
`nrot` | number of rotations used to compute the p-values.
`adjust.method` | method used to adjust the p-values for multiple testing. See `p.adjust` for possible values.
`midp` | logical, should mid-p-values be used in instead of ordinary p-values when adjusting for multiple testing?
`sort` | character, whether to sort output table by directional p-value (`"directional"`), non-directional p-value (`"mixed"`), or not at all (`"none"`).
`...` | other arguments are currently ignored.

### Details

These functions perform self-contained gene set tests against the null hypothesis that none of the genes in the set are differentially expressed. `fry` is the recommended function in the edgeR context.

The roast gene set test was proposed by Wu et al (2010) for microarray data and the `roast` and `mroast` methods documented here extend the test to digital gene expression data. The roast method uses residual space rotations instead of permutations to obtain p-values, a technique that take advantage of the full generality of linear models. The negative binomial count data is converted to approximate normal deviates by computing mid-p quantile residuals (Dunn and Smyth, 1996; Routledge, 1994) under the null hypothesis that the contrast is zero, and the normal deviates are then passed to the limma `roast` function. See `roast` for more description of the test and for a complete list of possible arguments. `mroast` is similar but performs `roast` tests for multiple of gene sets instead of just one.

The `fry` method documented here similarly generalizes the fry gene set test for microarray data. `fry` is recommended over `roast` or `mroast` for count data because, in this context, it is equivalent to `mroast` but with an infinite number of rotations.

### Value

`roast` produces an object of class `Roast`. See `roast` for details.

`mroast` and `fry` produce a data.frame. See `mroast` for details.

### Author(s)

Yunshun Chen and Gordon Smyth

### References

Dunn, PK, and Smyth, GK (1996). Randomized quantile residuals. J. Comput. Graph. Statist., 5, 236-244. http://www.statsci.org/smyth/pubs/residual.html

Routledge, RD (1994). Practicing safe statistics with the mid-p. Canadian Journal of Statistics 22, 103-110.

Wu, D, Lim, E, Francois Vaillant, F, Asselin-Labat, M-L, Visvader, JE, and Smyth, GK (2010). ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics 26, 2176-2182. http://bioinformatics.oxfordjournals.org/content/26/17/2176

### See Also

`roast`, `camera.DGEList`

### Examples

    mu <- matrix(10, 100, 4)
    group <- factor(c(0,0,1,1))
    design <- model.matrix(~group)

    # First set of 10 genes that are genuinely differentially expressed
    iset1 <- 1:10
    mu[iset1,3:4] <- mu[iset1,3:4]+10

    # Second set of 10 genes are not DE
    iset2 <- 11:20

    # Generate counts and create a DGEList object
    y <- matrix(rnbinom(100*4, mu=mu, size=10),100,4)
    y <- DGEList(counts=y, group=group)

    # Estimate dispersions
    y <- estimateDisp(y, design)

    roast(y, iset1, design, contrast=2)
    mroast(y, iset1, design, contrast=2)
    mroast(y, list(set1=iset1, set2=iset2), design, contrast=2)

[Package edgeR version 3.28.1 Index]