From f8644a8d96e474805acc0353ee576772a167575f Mon Sep 17 00:00:00 2001
From: hvaret <hugo.varet@pasteur.fr>
Date: Mon, 6 Apr 2020 16:24:27 +0200
Subject: [PATCH] round
---
DESCRIPTION | 2 +-
R/run.DESeq2.r | 6 +++++-
R/run.Limma.r | 7 ++++---
3 files changed, 10 insertions(+), 5 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index c179134..5441fb4 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: ChIPuanaR
Type: Package
Title: Differential analysis of ChIP-Seq data
Version: 0.99.0
-Date: 2020-01-13
+Date: 2020-04-06
Author: Marie-Agnes Dillies, Hugo Varet and Maëlle Daunesse
Maintainer: Maëlle Daunesse <maelle.daunesse@pasteur.fr>
Depends: R (>= 3.4.0), DESeq2, limma, kableExtra, knitr, ggplot2
diff --git a/R/run.DESeq2.r b/R/run.DESeq2.r
index 823f997..e36ec13 100755
--- a/R/run.DESeq2.r
+++ b/R/run.DESeq2.r
@@ -44,7 +44,11 @@ run.DESeq2 <- function(counts, conditions, batch=NULL, pAdjustMethod="BH", spike
colnames(counts.norm) <- paste0("norm.",colnames(counts))
res <- results(dds, contrast=c("conditions", levelTest, levelRef),
pAdjustMethod=pAdjustMethod, cooksCutoff=TRUE, independentFiltering=FALSE)
- res <- res[, c("baseMean", "log2FoldChange", "pvalue", "padj", "lfcSE", "stat")]
+ res <- res[, c("baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")]
+ res$baseMean <- round(res$baseMean, 2)
+ res$log2FoldChange <- round(res$log2FoldChange, 2)
+ res$lfcSE <- round(res$lfcSE, 2)
+ res$stat <- round(res$stat, 2)
resAnDif <- data.frame(counts, counts.norm, res)
results[[paste0(levelTest,"_vs_",levelRef)]] <- resAnDif
cat(paste("Comparison", levelTest, "vs", levelRef, "done\n"))
diff --git a/R/run.Limma.r b/R/run.Limma.r
index 8657330..9a4dc80 100644
--- a/R/run.Limma.r
+++ b/R/run.Limma.r
@@ -51,9 +51,10 @@ run.Limma <- function(counts, conditions, normalize.method="quantile", spikes=NU
fit2 <- contrasts.fit(fit=fit, contrasts=cont.matrix)
efit <- eBayes(fit=fit2)
colnames(v$E) <- paste0("norm.", colnames(counts))
- resAnDif <- data.frame(counts,v$E,
- baseMean=efit$Amean,
- log2FoldChange=as.numeric(efit$coefficients),
+ resAnDif <- data.frame(counts,
+ round(v$E, 2),
+ baseMean=round(efit$Amean, 2),
+ log2FoldChange=round(as.numeric(efit$coefficients), 2),
pvalue=as.numeric(efit$p.val),
padj=p.adjust(efit$p.value, method=pAdjustMethod))
results[[paste0(levelTest,"_vs_",levelRef)]] <- resAnDif
--
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