I'm very new to R and bioinformatics and I hope my question isnt that stupid... I'm trying to make a Heatmap with 200 DEGs from an RNA_Seq_Dataset. In my script (which I got from another PhD candidate) I've got the following code:
topVarianceGenes <- head(order(rowVars(assay(rld)), decreasing=T),200) matrix <- assay(rld)[topVarianceGenes,] matrix <- matrix - rowMeans(matrix) annotation_data <- as.data.frame(colData(rld)) pheatmap(matrix, scale = 'row', show_rownames = T, color = bluered(100), fontsize = 8, annotation_col = annotation_data, cluster_cols = F) `
It works quite well, but I'm told to use the Top Genes sort by logFC and I don't find anything using google or the search function in thi forum.
Thanks to anyone who could help! :)