hitselectionZscore: Selecting hits according to ZScores
In RNAither: Statistical analysis of high-throughput RNAi screens

Description Usage Arguments Details Value References See Also Examples

Selects significant genes according to their ZScore.

1 2	hitselectionZscore(dataset, col4zscore, col4sel, thresh, flag, flag2, col4anno, sumFunc, file4hits)

`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

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).

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.

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

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

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