hitselectionPval {RNAither} | R Documentation

## Selecting hits according to p-values

### Description

Selects significant genes according to their p-value.

### Usage

    hitselectionPval(dataset, pValVec, col4val, col4sel, thresh, col4anno, 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`
`col4val` | a character vector specifying a column of intensity values
`col4sel` | a character vector specifying the name of the new dataset column where hits will be stored
`thresh` | the threshold for the p-values, typically 0.05
`col4anno` | a character string specifying the name of the dataset column to be used to define the replicate, e.g. `"GeneName"` or `"Internal_GeneID"`
`file4hits` | the name of the file to store the results in

### Details

If there are no p-values under the defined threshold `thresh`, the threshold is increased to `min(pvalvec)`.

### 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
`replicaMatrix` | a matrix of replicates with corresponding values (as generated by `generateReplicateMat`)
`thresh` | the threshold for the p-values

P-values and the intensity values for each siRNA are stored in a text output file.

### See Also

`hitselectionZscore`, `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 <- hitselectionPval(scoredDataset1, pValVec1, "SigIntensity", "Pval_hits", 0.05,
    "GeneName", "pvalue_testfile1.txt")

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

[Package RNAither version 2.28.0 Index]