hclustCells: Cluster cells

In BPijuanSala/anSeq: Tools to analyse RNA-seq data

Description

Cluster cells using the spearman rank correlation as a similarity metric and (1-correlation)/2 as a distance metric.

Usage

hclustCells(data, clust.method = "ward.D2", leafreorder = "column",
  cor.method = "spearman")

Arguments

data	Dataframe or matrix containing the counts (genes x cells). The algorithm will cluster on these.
clust.method	Clustering method to use with hclust. Default: WarD2. For more options, see hclust.
leafreorder	Specify whether you want to obtain an hclust object with reordered gene ("row") or cell leaves ("column"). If you want to obtain both as a list, specify "both". Default: column (it will reorder the cells).
cor.method	correlation method to calculate the distance matrix.

Value

hclust object

Author(s)

Blanca Pijuan Sala.

References

hclust, order.optimal

See Also

hclust.

BPijuanSala/anSeq documentation built on May 30, 2019, 11:47 p.m.