hitselectionPval: Selecting hits according to 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 p-value.

1	hitselectionPval(dataset, pValVec, col4val, col4sel, thresh, col4anno, 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`
`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

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

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.

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

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