get_residuals {MethReg} | R Documentation |
Compute studentized residuals from fitting linear regression models to expression values in a data matrix
get_residuals(data, metadata.samples = NULL, metadata.genes = NULL, cores = 1)
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. |
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
A residuals matrix with samples as columns and features (gene, probes) as rows
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 )