giaever {GraphAT} | R Documentation

## Yeast Gene-Knockout Fitness Data

### Description

This data set contains fitness deficiency scores from gene knockout experiments involving yeast grown under a variety of altered environments (e.g. acid, heat, sorbitol, etc.)

### Usage

    data(giaever)

### Format

A matrix whose rows are the 5922 genes knocked out and whose columns are the 32 experimental conditions.

### Source

http://gobi.lbl.gov/YeastFitnessData

### References

Giaever, G. et al. 2002 ``Functional profiling of the Saccharomyces cerevisiae genome.'' Nature 418, 387–391.

### Examples

    data(giaever)

    ## Find the 3000 most variable genes, according to sd/mean:
    varMeas <- function(vec, na.rm=TRUE)
    {
        if(na.rm)
          vec <- vec[!is.na(vec)]
        if(length(vec) == 0)
          measure <- NA
        else
          measure <- sd(vec)/mean(vec)
        return(measure)
    }

    variability <- apply(giaever, 1, varMeas)

    rks <- rank(variability)

    giaever3000 <- giaever[rks>length(rownames(giaever))-3000,]

[Package GraphAT version 1.16.0 Index]