hitselectionPval {RNAither} | R Documentation |
Selects significant genes according to their p-value.
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]]