Cluster average methylation of multiple tracks
gpatterns.cluster_avg_meth(avgs, K, verbose = FALSE,
clust_order_func = partial(mean, na.rm = T), clust_columns = FALSE,
column_k = NULL, ret_hclust = FALSE, tidy = TRUE,
intra_clust_order = TRUE)
Arguments
- avgs
- avgs pre-computed intervals set with average methylation, output of gpatterns.get_avg_meth.
- K
- number of clusters for kmeans++
- verbose
- display kmeans++ messages
- clust_order_func
- order clusters by clust_order_func [default: mean]
- clust_columns
- cluster the columns (samples) using hclust
- column_k
- cut the hclust of the columns and return an additional
'samp_clust' column with the column cluster
- ret_hclust
- return a list with avgs (the clustering result) and
hc (the hclust object)
- tidy
- is the input tidy
- intra_clust_order
- order within each cluster using hclust (otherwise, the order would be by genomic position)
Value
if tidy: data frame with the following fields:
- 'chrom'
- 'start'
- 'end'
- 'ord'order of intervals within the cluster
- 'samp'sample id
- 'samp_clust'id of the column cluster (hclust cutree)
- 'clust'cluster id
- 'original columns'original columns of avgs (meth,unmeth,avg,cov)
if not tidy: data frame with the following fields:
- 'chrom'
- 'start'
- 'end'
- 'ord'order of intervals within the cluster
- 'samp_clust'id of the column cluster (hclust cutree)
- 'clust'cluster id
- 'original columns'original columns of avgs