Dear Biostarts community,
I am drawing a heatmap for gene clustering based on row variation, using the results from a standard DEseq2 pipeline.
I used the following code to pick top varied genes:
topVarGenes <- head(order(rowVars(assay(rld)), decreasing = TRUE), 100)
but the problems is that the head function skewed the results. I then changed the code to
topVarGenes <- rld[order(rowVars(assay(rld))), decreasing = TRUE, ]
then I got error:
Error in slot(object, slot_name) :
no slot of name "decreasing" for this object of class "DESeqTransform"
Can someone help me figure out what went wrong? I would very much appreciate that.
Thank you!
Wenhan
I have put the complete code below:
# pheatmap for gene clustering
library("genefilter")
library(pheatmap)
topVarGenes <- head(order(rowVars(assay(rld)), decreasing = TRUE), 100)
rld <- rld[order(rowVars(assay(rld)),decreasing = TRUE),]
topVarGenes <- rld[1:100,]
mat <- assay(rld)[ topVarGenes, ]
mat <- mat - rowMeans(mat)
anno <- as.data.frame(colData(rld))
row.names(mat) <- gsub('\\..+$', '', row.names(mat))
library(org.Hs.eg.db)
gns <- select(org.Hs.eg.db, row.names(mat), "SYMBOL", "ENSEMBL")
row.names(mat)[match(gns[,1], row.names(mat))] <- gns[,2]
png("gene_clustering_pheatmap.png", 1500, 3000, pointsize=25)
pheatmap(mat, annotation_col = anno, fontsize=24)
dev.off()
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dazhudou1122
Hi, you just need to do this, for selecting the top 100 most variable genes:
library(airway)
library(magrittr)
data('airway')
airway$dex %<>% relevel('untrt')
library('DESeq2')
dds <- DESeqDataSet(airway, design = ~ cell + dex)
dds <- DESeq(dds, betaPrior=FALSE)
rld <- rlog(dds)
top100 <- head(order(rowVars(assay(rld)), decreasing = TRUE), 100)
mat <- as.matrix(assay(rld)[top100,])
Thank you Kevin for your help. This is a very clean and elegant solution. It is working properly now.
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