MA or volcano plot for differential expression results

MA or volcano plot for differential expression results

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

Arguments

tags

tags returned by 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)