In fchuffar/dmethr: dmethr: a 3-step pipeline to explore DNA methylation controlled gene expression from omics data

source("../R/common.R")
layout(matrix(1:3,1), respect=TRUE)

plot_volcano(feats, gse, gs_name, main=paste0(gse, " - ", model))

gene_set = rownames(feats)[feats[[gs_name]]]
expression_vector = feats[,paste0("l2fc_", gse)]
names(expression_vector) = rownames(feats)
expression_vector = expression_vector[!is.na(expression_vector)]

utest = wilcox.test(expression_vector~ifelse(names(expression_vector)%in%gene_set, gs_name, "others"), las=2)
boxplot(rank(expression_vector)~ifelse(names(expression_vector)%in%gene_set, gs_name, "others"), main=paste0("Mann-Whitney U test (pval=", signif(utest$p.value, 3), ")"), ylab=paste0("rank(log2FoldChange)"), xlab="", col=adjustcolor(c("red", "grey"), alpha.f=.5))  

et_gsea_plot(expression_vector, gene_set, prefix=gs_name, nperm=3)

In a demethylating context, r gs_name genes are particularly upregulated. (A) The volcano plot shows the results of the differential analysis of r gse data for the model r model. The x-axis the represents the log2FoldChange of the model and the y-axis the the $-log10(pval_{Fisher})$. Red dots are the r gs_name genes. (B) The boxplot shows the distribution of genes ranks obtained from log2FoldChange for the r gs_name. The r gs_name genes are in red and the other genes are in grey. We perform the Mann-Whitney U test and conclude that r gs_name genes are particularly over expressed in the model r model with a significant pvalue of $r signif(utest$p.value, 3).$ (C) The enrichement plot is obtained using GSEA software. it illustrates that over expressed genes in r model are enriched in r gs_name genes.

fchuffar/dmethr documentation built on July 2, 2024, 1:17 a.m.