qqnorm-methods {DEDS} | R Documentation

## Normal Q-Q Plot for DEDS Objects

### Description

The function `qqnorm.DEDS` produces normal Quantile-Quantile plots of statistics for `DEDS-class` objects. The points corresponding to genes with DEDS q- or adjusted p-values less than a user defined threshold are highlighted.

### Usage

    ## S3 method for class 'DEDS':
    qqnorm(y, subset=c(1:nrow(y$stats)),
    xlab = "Quantiles of standard normal", thresh = 0.05, col = palette(), pch, ...)

### Arguments

`y` | An object of `DEDS`, produced by `deds.stat.linkC` or `deds.stat`.
`subset` | A numeric vector indicating the subset of points to be plotted.
`xlab` | A title for the x axis
`thresh` | A numeric variable specifying the threshold of significance in differential expression (DE) for q- or p-values of the DEDS object.
`col` | A specificatio for the colors to be used for plotting. It should have a length bigger than two. The first is used for points with q- or adjusted p-values smaller than the specified threshould (group I) and the second for points with q- or adjusted p-values bigger than the threshould (group II).
`pch` | A specification for the type of points to be used for plotting. It should have a length bigger than two. The first parameter is used for group I genes, and the second for group II genes.
`...` | Extra parameters for plotting.

### Details

The function `qqnorm.DEDS` implements a S3 method of `qqnorm` for `DEDS`. The `DEDS` class is a simple list-based class to store DEDS results and `qqnorm.DEDS` is used for a DEDS object that is created by functions `deds.stat`, `deds.stat.linkC`. The list contains a "stat" component, which stores statistics from various statistical tests. The function `qqnorm.DEDS` extracts the "stat" component and produces a normal QQ plot for each type of statistics. `qqnorm.DEDS` as a default highlights points (corresponding to genes) with DEDS adjusted p- or q-values less than a user defined threshold.

For DEDS objects that are created by the function `deds.pval`, the "stat" matrix consists of unadjusted p-values from different statistical models. For graphical display of these p values, the user can use `hist.DEDS` and `pairs.DEDS`.

### Author(s)

Yuanyuan Xiao, yxiao@itsa.ucsf.edu,
Jean Yee Hwa Yang, jean@biostat.ucsf.edu.

### See Also

`deds.stat`, `deds.pval`, `deds.stat.linkC`, `hist.DEDS`, `qqnorm.DEDS`

### Examples

    X <- matrix(rnorm(1000,0,0.5), nc=10)
    L <- rep(0:1,c(5,5))

    # genes 1-10 are differentially expressed
    X[1:10,6:10]<-X[1:10,6:10]+1
    # DEDS summarizing t, fc and sam
    d <- deds.stat.linkC(X, L, B=200)

    # qqnorm for t, fc and sam
    qqnorm(d)
    # change points color
    qqnorm(d, col=c(2,3))
    # change points type
    qqnorm(d, pch=c(1,2))

[Package DEDS version 1.12.1 Index]