| collapseTranscripts {ballgown} | R Documentation |
cluster a gene's transcripts and calculate cluster-level expression
collapseTranscripts(gene, gown, meas = "FPKM", method = c("hclust",
"kmeans"), k = NULL)
gene |
which gene's transcripts should be clustered |
gown |
ballgown object |
meas |
which transcript-level expression measurement to use
( |
method |
which clustering method to use: |
k |
how many clusters to use. |
list with two elements:
tab, a cluster-by-sample table of expression measurements
(meas, either cov or FPKM), where the expression measurement for
each cluster is the mean (for 'cov') or aggregate (for
'FPKM', as in gexpr) expression measurement for all
the transcripts in that cluster. This table can be used as the
gowntable argument to stattest, if differential
expression results for transcript *clusters* are desired.
cl output from clusterTranscripts that was run
to produce tab, for reference. Cluster IDs in the cluster
component correspond to row names of tab
Alyssa Frazee
hclust, kmeans,
clusterTranscripts, plotLatentTranscripts
data(bg) collapseTranscripts(bg, gene='XLOC_000454', meas='FPKM', method='kmeans')