clusterTranscripts {ballgown} | R Documentation |
group a gene's assembled transcripts into clusters
clusterTranscripts(gene, gown, k = NULL, method = c("hclust", "kmeans"))
gene |
name of gene whose transcripts will be clustered. When using
Cufflinks output, usually of the form |
gown |
ballgown object containing experimental data |
k |
number of clusters to use |
method |
clustering method to use. Must be one of |
list with elements clusters
and pctvar
.
clusters
contains columns "cluster" and "t_id", and denotes which
transcripts belong to which clusters.
pctvar
is only non-NULL when using k-means clustering and is the
percentage of variation explained by these clusters, defined as the ratio
of the between-cluster sum of squares to the total sum of squares.
Alyssa Frazee
hclust
, kmeans
,
plotLatentTranscripts
for visualizing the transcript clusters
data(bg) clusterTranscripts('XLOC_000454', bg, k=2, method='kmeans') # transcripts 1294 and 1301 cluster together, 91% variation explained.