clusters_per_read: Obtain a series of tandem repeat unit clusters per sequencing...

In arnederoeck/NanoSatelliteR: QC, plotting, and clustering of tandem repeat segmentation created by NanoSatellite.

Description

clusters_per_read() extracts the cluster per tandem repeat unit and concatenates them according to their original sequence in the sequencing read.

Usage

clusters_per_read(tsclust_obj)

Arguments

tsclust_obj

A tsclust object generated by dtwclust::tsclust()

Details

This function uses a tsclust object generated by dtwclust::tsclust() and returns a data.frame containing a comma-separated series of tandem repeat unit clusters.

Examples

df <- load_summary("/storage/NanoSatellite_chunks/")
qc <- summary_qc(df)
df2 <- qual_reads(df,qc$center_cutoff)
squiggles <- load_squiggles("/storage/NanoSatellite_chunks/",df2)

library(doParallel)
library(dtwclust)
k_clusters=2
registerDoParallel(cores=8)

positive_clustering=tsclust(squiggles$positive,type="h",k=k_clusters,trace=TRUE,distance = "dtw_basic", control=hierarchical_control(method="ward.D",symmetric = T))

cpr=clusters_per_read(positive_clustering)

arnederoeck/NanoSatelliteR documentation built on May 6, 2019, 1:35 a.m.