hitselectionZscore {RNAither} | R Documentation

## Selecting hits according to ZScores

### Description

Selects significant genes according to their ZScore.

### Usage

    hitselectionZscore(dataset, col4zscore, col4sel, thresh, flag, flag2, col4anno,
    sumFunc, file4hits)

### Arguments

`dataset` | an R data frame generated with `generateDatasetFile`
`col4zscore` | a character vector specifying the name of the column containing the ZScores, usually `SigIntensity`
`col4sel` | a character vector specifying the name of the new dataset column where hits will be stored
`thresh` | the threshold for the ZScores. The interpretation depends on the choice of the parameter `flag2`.
`flag` | 1 or 2. 1 means the ZScores are kept per well, 2 that they are summarized according to the parameter `sumFunc`.
`flag2` | 1, 2 or -2. If 1 is chosen and `thresh` == n, then the n greatest Zscores are chosen as hits. If 1 is chosen and `thresh` == -n, then the n smallest Zscores are chosen. If 1 is chosen and `thresh` == 0, all ZScores are chosen and written to the output file. If 2 is chosen, all Zscores greater than or equal to `thresh` are chosen. If -2 is chosen, all Zscores smaller than or equal to `thresh` are chosen.
`col4anno` | a character string specifying the name of the dataset column to be used to define the replicate, for example `"GeneName"` or `"Internal_GeneID"`
`sumFunc` | the function used to summarize ZScore values, e.g. `mean` or `median`.
`file4hits` | the name of the file to store the results in

### Details

If `flag2` == -2, and there are no ZScores under the defined threshold `thresh`, the threshold is increased to `min(ZScores)`.

If `flag2` == 2, and there are no ZScores over the defined threshold `thresh`, the threshold is increased to `max(ZScores)`.

### Value

A list containing:

`dataset` | the dataset with an added column defining the hits in the form of a binary vector
`hitVector` | the binary vector itself
`thresh` | the threshold for the ZScores

ZScores are stored in a text output file.

### References

N. Malo et al. Statistical practice in high-throughput screening data analysis. Nature Biotech, 24(2): 167-175, 2006.

### See Also

`hitselectionPval`, `hitselectionZscorePval`, `Ttest`

### Examples

    data(scoredDataset1, package="RNAither")
    data(pValVec1, package="RNAither")

    ##for details on the generation of pValVec1 and scoredDataset1, see the example of the Ttest function linked above.

    scoredHits1 <- hitselectionZscore(scoredDataset1, "SigIntensity", "Zscore_hits", -10,
    2, 1, "GeneName", median, "Zscores_testfile1.txt")

    newdataset <- scoredHits1[[1]]
    hitvector <- scoredHits1[[2]]

[Package RNAither version 2.30.1 Index]