hclustCells: Cluster cells

Description Usage Arguments Value Author(s) References See Also

View source: R/function_hclustCells.R

Description

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

Usage

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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 Oct. 10, 2018, 7:20 p.m.