balance {Pigengene} | R Documentation

## Balances the number of samples

### Description

Oversamples data by repeating rows such that each condition has roughly the same number of samples.

### Usage

         balance(Data, Labels, amplification = 5, verbose = 0, naTolerance=0.05)

### Arguments

`Data` | A matrix or data frame containing the expression data, with genes corresponding to columns and rows corresponding to samples. Rows and columns must be named.
`Labels` | A (preferably named) vector containing the Labels (condition types) for `Data`. Names must agree with rows of `Data`.
`amplification` | An integer that controls the number of repeats for each condition. The number of all samples roughly will be multiplied by this factor after oversampling.
`verbose` | The integer level of verbosity. 0 means silent and higher values produce more details of computation.
`naTolerance` | Upper threshold on the fraction of entries per gene that can be missing. Genes with a larger fraction of missing entries are ignored. For genes with smaller fraction of NA entries, the missing values are imputed from their average expression in the other samples. See `check.pigengene.input`.

### Value

A list of:

`balanced` | The matrix of oversampled data
`Reptimes` | A vector of integers named by conditions reporting the number of repeats for each condition.
`origSampleInds` | The indices of rows in `balanced` that correspond to the original samples before oversampling

### Author(s)

Habil Zare

### See Also

`Pigengene-package`, `one.step.pigengene`, `wgcna.one.step`, `compute.pigengene`

### Examples

         data(aml)
         data(mds)
         d1 <- rbind(aml,mds)
         Labels <- c(rep("AML",nrow(aml)),rep("MDS",nrow(mds)))
         names(Labels) <- rownames(d1)
         b1 <- balance(Data=d1, Labels=Labels)
         d2 <- b1$balanced

[Package Pigengene version 1.12.0 Index]