hitselectionZscore {RNAither} | R Documentation |
Selects significant genes according to their ZScore.
hitselectionZscore(dataset, col4zscore, col4sel, thresh, flag, flag2, col4anno, sumFunc, file4hits)
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 |
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)
.
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.
N. Malo et al. Statistical practice in high-throughput screening data analysis. Nature Biotech, 24(2): 167-175, 2006.
hitselectionPval
, 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 <- hitselectionZscore(scoredDataset1, "SigIntensity", "Zscore_hits", -10, 2, 1, "GeneName", median, "Zscores_testfile1.txt") newdataset <- scoredHits1[[1]] hitvector <- scoredHits1[[2]]