hitselectionZscorePval {RNAither} | R Documentation |
Selects significant genes according to their ZScore (summarized with the gene median) and p-values.
hitselectionZscorePval(dataset, pValVec, col4zscore, col4sel, thresh, thresh2, flag2, col4anno, sumFunc, 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 |
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 |
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.
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.
hitselectionPval
, hitselectionZscore
, 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 <- hitselectionZscorePval(scoredDataset1, pValVec1, "SigIntensity", "Zscore_pval_hits", -1.5, 0.05, -2, "GeneName", median, "Zscores_pvals_testfile1.txt") newdataset <- scoredHits1[[1]] hitvector <- scoredHits1[[2]]