hitselectionZscorePval: Selecting hits according to ZScores and p-values
In RNAither: Statistical analysis of high-throughput RNAi screens

Description Usage Arguments Details Value See Also Examples

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

1 2	hitselectionZscorePval(dataset, pValVec, col4zscore, col4sel, thresh, thresh2, flag2, col4anno, sumFunc, file4hits)

`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

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.

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.

hitselectionPval, hitselectionZscore, Ttest

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]]