rankProbes {mCSEA} | R Documentation

## Rank CpG probes

### Description

Apply a linear model to Illumina's 450k or EPIC methylation data to get the t-value of each CpG probe

### Usage

    rankProbes(methData, pheno = NULL, paired = FALSE, explanatory = 1,
      covariates = c(), pairColumn = c(), caseGroup = 1, refGroup = 2,
      continuous = NULL, typeInput = "beta", typeAnalysis = "M")

### Arguments

`methData` | A data frame or a matrix containing Illumina's CpG probes in rows and samples in columns. A SummarizedExperiment object can be used too
`pheno` | A data frame or a matrix containing samples in rows and covariates in columns. If NULL (default), pheno is extracted from the SummarizedExperiment object
`paired` | Perform a paired t-test (default = FALSE)
`explanatory` | The column name or position from pheno used to perform the comparison between groups (default = first column)
`covariates` | A list or character vector with column names from pheno used as data covariates in the linear model
`pairColumn` | Only for paired analysis. The column name or position from pheno used to connect the paired samples (default = NULL)
`caseGroup` | The group name or position from explanatory variable used as cases to perform the comparison (default = first group)
`refGroup` | The group name or position from explanatory variable used as reference to perform the comparison (default = second group)
`continuous` | A list or character vector with columns names from pheno which should be treated as continuous variables (default = none)
`typeInput` | Type of input methylation data. "beta" for Beta-values and "M" for M-values
`typeAnalysis` | "M" to use M-values to rank the CpG probes (default). "beta" to use Beta-values instead

### Value

A named vector containing the t-values from the linear model for each CpG probe

### Author(s)

Jordi Martorell Marugán, jordi.martorell@genyo.es

### References

Smyth, G. K. (2005). Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions using R and Bioconductor, 397-420.

### See Also

`mCSEATest`

### Examples

    data(mcseadata)
    myRank <- rankProbes(betaTest, phenoTest, refGroup = "Control")
    head(myRank)

[Package mCSEA version 1.12.0 Index]