RNAither (version 2.20.0)

hitselectionPval: 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

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.

Details

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

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]]