get_residuals {MethReg} | R Documentation

## Get residuals from regression model

### Description

Compute studentized residuals from fitting linear regression models to expression values in a data matrix

### Usage

    get_residuals(data, metadata.samples = NULL, metadata.genes = NULL, cores = 1)

### Arguments

`data` | A matrix or SummarizedExperiment object with samples as columns and features (gene, probes) as rows. Note that expression values should typically be log2(expx + 1) transformed before fitting linear regression models.
`metadata.samples` | A data frame with samples as rows and columns the covariates. No NA values are allowed, otherwise residual of the corresponding sample will be NA.
`metadata.genes` | A data frame with genes (covariates) as rows and samples as columns. For each evaluated gene, each column (e.g. CNA) that corresponds to the same gene will be set as a single covariate variable. This can be used to correct copy number alterations for each gene.
`cores` | Number of CPU cores to be used. Defaults to 1.

### Details

When only `metadata.samples` are provided, this function computes residuals for expression values in a data matrix by fitting model

`features ~ Sample_covariate1 + Sample_covariate2 ... + Sample_covariateN` where `N` is the index of the columns in the metadata provided, `features` are (typically log transformed) expression values.

When the user additionally provide `metadata.genes`, that is, gene metadata (e.g. gene_covariate = copy number variations/alterations) residuals are computed by fitting the following model:

`features ~ Sample_covariate1 + Sample_covariate2 ... + Sample_covariateN + gene_covariate`

### Value

A residuals matrix with samples as columns and features (gene, probes) as rows

### Examples

    data("gene.exp.chr21.log2")

    data("clinical")
    metadata <- clinical[,c( "gender", "sample_type")]

    cnv <- matrix(
       sample(x = c(-2,-1,0,1,2),
       size = ncol(gene.exp.chr21.log2) * nrow(gene.exp.chr21.log2),replace = TRUE),
       nrow = nrow(gene.exp.chr21.log2),
       ncol = ncol(gene.exp.chr21.log2)
    )
    rownames(cnv) <- rownames(gene.exp.chr21.log2)
    colnames(cnv) <- colnames(gene.exp.chr21.log2)

    gene.exp.residuals <- get_residuals(
       data = gene.exp.chr21.log2[1:3,],
       metadata.samples = metadata,
       metadata.genes = cnv
    )
    gene.exp.residuals <- get_residuals(
       data = gene.exp.chr21.log2[1:3,],
       metadata.samples = metadata,
       metadata.genes = cnv[1:2,]
    )
    gene.exp.residuals <- get_residuals(
       data = gene.exp.chr21.log2[1:3,],
       metadata.samples = metadata
    )

[Package MethReg version 1.2.1 Index]