calculateContrasts {NormalyzerDE} | R Documentation

## Performs statistical comparisons between the supplied conditions. It uses the design matrix and data matrix in the supplied NormalyzerStatistics object. A column is supplied specifying which of the columns in the design matrix that is used for deciding the sample groups. The comparisons vector specifies which pairwise comparisons between condition levels that are to be calculated.

### Description

Optionally, a batch column can be specified allowing compensation for covariate variation in the statistical model. This is only compatible with a Limma-based statistical analysis.

### Usage

    calculateContrasts(nst, comparisons, condCol, batchCol = NULL,
      splitter = "-", type = "limma", leastRepCount = 1)

    ## S4 method for signature 'NormalyzerStatistics'
    calculateContrasts(nst, comparisons,
      condCol, batchCol = NULL, splitter = "-", type = "limma",
      leastRepCount = 1)

### Arguments

`nst` | Results evaluation object.
`comparisons` | String with comparisons for contrasts.
`condCol` | Column name in design matrix containing condition information.
`batchCol` | Column name in design matrix containing batch information.
`splitter` | Character dividing contrast conditions.
`type` | Type of statistical test (Limma or welch).
`leastRepCount` | Least replicates in each group to be retained for contrast calculations

### Value

nst Statistics object with statistical measures calculated

### Examples

    data(example_stat_summarized_experiment)
    nst <- NormalyzerStatistics(example_stat_summarized_experiment)
    results <- calculateContrasts(nst, c("1-2", "2-3"), "group")
    resultsBatch <- calculateContrasts(nst, c("1-2", "2-3"), "group", batchCol="batch")

[Package NormalyzerDE version 1.6.0 Index]