RNAither (version 2.20.0)

hitselectionZscore: 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

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.

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).

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]]