filter_exp_by_quant_mean_FC: Select genes with variations above a threshold

In MethReg: Assessing the regulatory potential of DNA methylation regions or sites on gene transcription

Description

For each gene, compares the mean gene expression levels in samples in high expression (Q4) vs. samples with low gene expression (Q1), and requires the fold change to be above a certain threshold.

Usage

filter_exp_by_quant_mean_FC(exp, fold.change = 1.5, cores = 1)

Arguments

exp	Gene expression matrix or SumarizedExperiment object
fold.change	Threshold for fold change of mean gene expression levels in samples with high (Q4) and low (Q1) gene expression levels. Defaults to 1.5.
cores	Number of CPU cores to be used in the analysis. Default: 1

Value

A subset of the original matrix only with the rows passing the filter threshold.

Examples

data("gene.exp.chr21.log2")
gene.exp.chr21.log2.filtered <- filter_exp_by_quant_mean_FC(
  gene.exp.chr21.log2
)

MethReg documentation built on Nov. 8, 2020, 8:01 p.m.