seekDEcluster: PCA, heatmap and sample distance matrix

In Solatar/seeqR:

Description

Imports: DESeq2, limma, vsn, pheatmap, SummarizedExperiment, ggplot2, ggpubr

Usage

seekDEcluster(
  dds,
  Title = "",
  transformation = "rlog",
  removeBatchEffect = FALSE,
  heatmapN = 20,
  heatmapClusterCols = F
)

Arguments

dds	DESeq object: can be obtained as 3rd item from seekDEseq(), or from the normal DESeq2 pipeline
Title	string: a title for the final figure
transformation	string: what transformation to use ("rlog", "vst" or "norm"). Check which is best by using clTrans()
removeBatchEffect	boolean: TRUE removes the batch effect
nHeatmap	integer: number of genes to consider in the heatmap

Value

ggarrange object with 3 ggpplots to determine clustering of the samples.

Examples

Counts
myGroup <- c(1,1,2,1,2,2) #(e.g. you have WT,WT,KO,WT,KO,KO)
myBatch <- c(1,1,1,2,2,2)
myDE <- seekDeseq(Counts = myCounts, Groups = myGroups)
myDEcluster <- seekDEcluster(myDE[[3]])

Solatar/seeqR documentation built on Feb. 19, 2021, 8:07 p.m.