Commit f0a81668 authored by khalid's avatar khalid
Browse files

DESeq2 now output top40 genes without filtering

parent 1ed6822d
......@@ -72,14 +72,17 @@ if (sum(keep) < 1000) {
vsd = varianceStabilizingTransformation(dds)
} else {
vsd <- vst(dds, blind=FALSE)
}
}
dat <- plotPCA(vsd, intgroup="condition",returnData=TRUE)
dat <- plotPCA(vsd, intgroup="condition",returnData=TRUE)
percentVar <- round(100 * attr(dat, "percentVar"))
png(filename = snakemake@output[["PCA"]], height=800, width=800)
p <- ggplot(dat,aes(x=PC1,y=PC2,col=group))
p + geom_point() + ggtitle("PCA on normalized, variance-stabilized transformed counts")
p + geom_point(size=3) + xlab(paste0("PC1: ",percentVar[1],"% variance")) +
ylab(paste0("PC2: ",percentVar[2],"% variance")) +
coord_fixed() + ggtitle("PCA on normalized, variance-stabilized transformed counts")
dev.off()
# cpm_counts = cpm(txi$counts)
......@@ -91,16 +94,18 @@ dev.off()
options(digit=4)
resSig <- subset(res, padj < 0.1)
resSigdf = data.frame(resSig@listData,row.names = resSig@rownames)
# resSig <- subset(res, padj < 0.1)
# resSigdf = data.frame(resSig@listData,row.names = resSig@rownames)
#datatable(resSigdf,options = list(scrollX = '300px'))
topGenes = head(resSigdf[order(resSigdf$padj),], 40)
#topGenes = head(resSigdf[order(resSigdf$padj),], 40)
#top 40 genes basé sur les p-values
topGenes = head(as.data.frame(res[order(res$pvalue),]) , 40)
cat("# id: Top_genes
# section_name: 'Top 40 genes'
# description: 'Tableau des 40 top genes'
# description: 'Tableau des 40 top genes avec les plus faibles pvalues'
# format: 'tsv'
# plot_type: 'table'\ngene\t", file=snakemake@output[["Top_genes"]])
......
......@@ -5,7 +5,7 @@
website: "https://bioconductor.org/packages/release/bioc/html/DESeq2.html",
git: "git clone https://git.bioconductor.org/packages/DESeq2",
description: "Differential gene expression analysis based on the negative binomial distribution. Using normalized count data.",
version: "3\.10",
version: "3.10",
documentation: "https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf",
multiqc: "custom",
commands:
......
......@@ -78,11 +78,11 @@
],
install:
{
limma: ['Rscript -e ''BiocManager::install("limma", version = "3.8",Ncpus=8, clean=TRUE);library("limma")'''],
edger: ['Rscript -e ''BiocManager::install("edgeR", version = "3.8",Ncpus=8, clean=TRUE);library("edgeR")'''],
tximport: ['Rscript -e ''BiocManager::install("tximport", version = "3.8",Ncpus=8, clean=TRUE);library("tximport")'''],
rhdf5: ['Rscript -e ''BiocManager::install("rhdf5", version = "3.8",Ncpus=8, clean=TRUE);library("rhdf5")'''],
GenomicFeatures: ['Rscript -e ''BiocManager::install("GenomicFeatures", version = "3.8",Ncpus=8, clean=TRUE);library("GenomicFeatures")'''],
limma: ['Rscript -e ''BiocManager::install("limma", version = "3.10",Ncpus=8, clean=TRUE);library("limma")'''],
edger: ['Rscript -e ''BiocManager::install("edgeR", version = "3.10",Ncpus=8, clean=TRUE);library("edgeR")'''],
tximport: ['Rscript -e ''BiocManager::install("tximport", version = "3.10",Ncpus=8, clean=TRUE);library("tximport")'''],
rhdf5: ['Rscript -e ''BiocManager::install("rhdf5", version = "3.10,Ncpus=8, clean=TRUE);library("rhdf5")'''],
GenomicFeatures: ['Rscript -e ''BiocManager::install("GenomicFeatures", version = "3.10",Ncpus=8, clean=TRUE);library("GenomicFeatures")'''],
pheatmap: ['Rscript -e ''install.packages("pheatmap",Ncpus=8, clean=TRUE);library("pheatmap"))''']
},
script: edger.script.R,
......
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