draw_DEGs: MA or volcano plot for differential expression results

In OceaneCsn/DIANE: DIANE

MA or volcano plot for differential expression results

Description

MA or volcano plot for differential expression results

Usage

draw_DEGs(tags, fdr = 0.01, lfc = 0, MA = TRUE)

Arguments

tags	tags returned bu estimateDEGs, function, that is to say topTags from edgeR, used with p.value = 1
fdr	pvalue for DEGs detection
lfc	absolute log fold change threshold for differentially expressed genes, default is 0.
MA	TRUE : MA plot (LogFC depending on average log expression), or else "Volcano" for FDR depending on logFC.

Examples

data("abiotic_stresses")
tcc_object <- DIANE::normalize(abiotic_stresses$raw_counts, abiotic_stresses$conditions, 
iteration = FALSE)
tcc_object <- DIANE::filter_low_counts(tcc_object, 10*length(abiotic_stresses$conditions))
fit <- DIANE::estimateDispersion(tcc = tcc_object, conditions = abiotic_stresses$conditions)
tags <- DIANE::estimateDEGs(fit, reference = "C", perturbation = "H", p.value = 1)
DIANE::draw_DEGs(tags, fdr = 0.01, lfc = 1)

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