rankProbes: Rank CpG probes

In jordimartorell/mCSEA: Methylated CpGs Set Enrichment Analysis

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, [e-mail]

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)

jordimartorell/mCSEA documentation built on Dec. 8, 2024, 10:32 a.m.