stat.gnames {sma} | R Documentation

## Sort Genes According to the Value of a Statistic

### Description

Lists genes and corresponding statistics in decreasing order of the statistics. This function applies to any type of statistic, including log ratios, one and two-sample t-statistics, and F-statistics. Missing values are ignored, as in `sort(..., na.last=NA)`.

### Usage

    stat.gnames(x, gnames, crit=0.05)

### Arguments

`x` | a numeric vector containing the statistics for each gene. Missing values (NAs) are allowed.
`gnames` | a character vector containing the gene names.
`crit` | specifies the number of genes to be returned. If crit < 1, the crit*100% genes with the largest x values are listed. If crit >= 1, the crit genes with the largest x values are listed.

### Value

List containing the following components

`gnames` | gene names sorted in decreasing order of the statistics in x.
`t` | statistics sorted in decreasing order.

### Author(s)

Yee Hwa Yang, yeehwa@stat.berkeley.edu
Sandrine Dudoit, sandrine@stat.berkeley.edu

### See Also

`stat.t2`, `order`, `sort`.

### Examples

    ## Calculating log ratio and performing a t test.
    data(MouseArray)
    ## mouse.setup <- init.grid()
    ## mouse.data <- init.data() ## see \emph{init.data}
    mouse.lratio <- stat.ma(mouse.data, mouse.setup)
    cl <- c(rep(1,3), rep(2,3))
    mouse.t2 <- stat.t2(mouse.lratio, cl)

    ## Looking at gene names
    ## Finding the top 10 t-statistics
    stat.gnames(abs(mouse.t2$t), mouse.gnames, crit=10)

    ## Finding the top 1
    stat.gnames(abs(mouse.t2$t), mouse.gnames, crit=0.01)

    ## Finding the 10 extreme M values in the first slide
    stat.gnames(abs(mouse.lratio$M[, 1]), mouse.gnames, crit=10)

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