estimateDEGs: Estimates Differentially Expression Genes

In OceaneCsn/DIANE: DIANE

Estimates Differentially Expression Genes

Description

Given a glmFit model, performs log ratio tests using edgeR function glmLRT and returns the genes that are differentially expressed between the reference and perturbation conditions. log ratios are expressed as log(perturbation/reference)

Usage

estimateDEGs(fit, reference, perturbation, p.value = 1, lfc = 0)

Arguments

fit	edgeR glmFit
reference	condition being considered as the reference for differential analysis. It should corresponds to a condition name, e.g. the string before the underscore and replicate number in your sample names.
perturbation	condition we compared to the reference for differential analysis. It should corresponds to a condition name, e.g. the string before the underscore and replicate number in your sample names.
p.value	numeric cutoff value for adjusted p-values. Only tags with adjusted p-values equal or lower than specified are returned
lfc	minimal absolute log fold change required for a gene to be considered as differentially expressed.

Value

topTags object, which table element contains DEGs dataframe.

Examples

data("abiotic_stresses")
tcc_object <- DIANE::normalize(abiotic_stresses$raw_counts, 
abiotic_stresses$conditions, iteration = FALSE)
threshold = 10*length(abiotic_stresses$conditions)
tcc_object <- DIANE::filter_low_counts(tcc_object, threshold)
fit <- DIANE::estimateDispersion(tcc = tcc_object, 
conditions = abiotic_stresses$conditions)
topTags <- DIANE::estimateDEGs(fit, reference = "C", perturbation = "H", p.value = 0.01)
DEGs <- topTags$table
head(DEGs)

OceaneCsn/DIANE documentation built on Jan. 10, 2024, 6:43 p.m.