collapseTranscripts {ballgown}R Documentation

cluster a gene's transcripts and calculate cluster-level expression

Description

cluster a gene's transcripts and calculate cluster-level expression

Usage

collapseTranscripts(
  gene,
  gown,
  meas = "FPKM",
  method = c("hclust", "kmeans"),
  k = NULL
)

Arguments

gene

which gene's transcripts should be clustered

gown

ballgown object

meas

which transcript-level expression measurement to use ('cov', average per-base coverage, or 'FPKM')

method

which clustering method to use: 'hclust' (hierarchical clustering) or 'kmeans' (k-means clustering).

k

how many clusters to use.

Value

list with two elements:

Author(s)

Alyssa Frazee

See Also

hclust, kmeans, clusterTranscripts, plotLatentTranscripts

Examples

data(bg)
collapseTranscripts(bg, gene='XLOC_000454', meas='FPKM', method='kmeans')


[Package ballgown version 2.25.1 Index]