hitselectionZscorePval {RNAither} | R Documentation

## Selecting hits according to ZScores and p-values

### Description

Selects significant genes according to their ZScore (summarized with the gene median) and p-values.

### Usage

    hitselectionZscorePval(dataset, pValVec, col4zscore, col4sel, thresh, thresh2,
    flag2, col4anno, sumFunc, file4hits)

### Arguments

`dataset` | an R data frame generated with `generateDatasetFile`
`pValVec` | a vector of p-values, as generated by one of the test functions `Ttest`, `MannWhitney` or `RankProduct`
`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`.
`thresh2` | the threshold for the p-values
`flag2` | 2 or -2. 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 there are no p-values under the defined threshold `thresh2`, it is increased to `min(pvalvec)`.

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

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

If there are not hits for the combined threshold of p-values and ZScores, the ZScore threshold is changed until there is a hit.

### 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
`thresh2` | he threshold for the p-values

ZScores and p-values are stored in a text output file.

### See Also

`hitselectionPval`, `hitselectionZscore`, `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 <- hitselectionZscorePval(scoredDataset1, pValVec1, "SigIntensity",
    "Zscore_pval_hits", -1.5, 0.05, -2, "GeneName", median, "Zscores_pvals_testfile1.txt")

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

[Package RNAither version 2.35.0 Index]