RNAither (version 2.20.0)

incorporatepValVec: Incorporate a vector of p-values into a dataset

Description

Incorporates a vector of p-values into a dataset. Also works with a dataset containing values per well (non summarized), or with a hit vector.

Usage

incorporatepValVec(dataset, pValVec, replicaMatrix, col4anno, colname4pval)

Arguments

dataset

an R data frame generated with generateDatasetFile

pValVec

a vector of p-values

replicaMatrix

a matrix of replicate values, as generated by generateReplicateMat

col4anno

a character string specifying the name of the dataset column to be used to define the replicate, for example "GeneName" or "Internal_GeneID"

colname4pval

a character string specifying the name of the dataset column the p-values will be stored in

Value

Returns the dataset with an added column of p-values.

See Also

multTestAdjust, Ttest

Examples

data(exampleDataset, package="RNAither")

data(scoredDataset1, package="RNAither")
##scoredDataset1 already contains the p-value column
data(pValVec1, package="RNAither")

##for details on the generation of pValVec1 and scoredDataset1, see the example of the Ttest function linked above.

temp <- generateReplicateMat(dataset, 1, "Intensities", "SigIntensity",  "GeneName")
replicamatrix <- temp[[1]]
newdataset <- incorporatepValVec(dataset, pValVec1, replicamatrix, "GeneName", "pvals")
##newdataset and scoredDataset1 are now equivalent