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)

[Package sma version 0.5.15 Index]