generateReplicateMat: Generate a matrix of replicates

Description

Generates a matrix out of a dataset, each row corresponding to an siRNA/gene ID, each column to a channel value or its index in the dataset.

Usage

generateReplicateMat(data, minNbReps, IndexOrInt, col4val, col4anno)

Arguments

data

an R data frame generated with generateDatasetFile

minNbReps

set to 2 if you want to exclude replicates occurring only once in the dataset, otherwise 1.

IndexOrInt

a character string - either "Index" or "Intensities" - specifying which values are to be contained in the output matrix.

col4val

a character string specifying the name of the dataset column to be used for the values of the output matrix (if IndexOrIntensities is set to "Intensities"), for example "SigIntensity" or "NbCells"

col4anno

a character string specifying the name of the dataset column to be used for the output matrix' rows, for example "GeneName" or "Internal_GeneID".

Value

A matrix with each row corresponding to an siRNA/gene ID (as reflected in rownames), each column to a channel value or its index in the dataset. Missing values (in case of different number of replicates occuring for different siRNAs/genes) are set to NA.

Details

The function will omit values or indexes of lines/wells whose value in the column specified by colname4val is set to NA, (which is the case if the spot type is set to -1). If you do not want to omit those, use generateRepMatNoFilter.

Examples

Run this code

data(exampleDataset, package="RNAither")

replicatematrix <- generateReplicateMat(dataset, 2, "Index", "SigIntensity",  "GeneName")