hitselectionZscorePval {RNAither}R Documentation

Selecting hits according to ZScores and p-values

Description

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

Usage

hitselectionZscorePval(dataset, pValVec, col4zscore, col4sel, thresh, thresh2, 
flag2, col4anno, sumFunc, 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
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

Details

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.

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
thresh2 he threshold for the p-values

ZScores and p-values are stored in a text output file.

See Also

hitselectionPval, hitselectionZscore, 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 <- hitselectionZscorePval(scoredDataset1, pValVec1, "SigIntensity", 
"Zscore_pval_hits", -1.5, 0.05, -2, "GeneName", median, "Zscores_pvals_testfile1.txt")

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

[Package RNAither version 1.4.6 Index]