SaaRclust: Wrapper function to run saarclust pipeline for a given number...

In daewoooo/SaaRclust: R Package to cluster long sequencing reads into chromosomes to facilitate de novo genome assembly.

Description

Wrapper function to run saarclust pipeline for a given number of long reads reads.

Usage

SaaRclust(minimap.file = NULL, outputfolder = "SaaRclust_results",
  num.clusters = 47, EM.iter = 100, alpha = 0.1, minLib = 10,
  upperQ = 0.95, theta.param = NULL, pi.param = NULL, logL.th = 1,
  theta.constrain = FALSE, store.counts = FALSE, HC.input = NULL,
  cellNum = NULL, log.scale = FALSE)

Arguments

minimap.file	A path to the minimap file to load.
outputfolder	A folder name to export the results.
num.clusters	Expected number of clusters. (for 22 autosomes == 44 clusters)
EM.iter	Number of iteration to run EM for.
alpha	Estimated level of background in Strand-seq reads.
minLib	Minimal number of StrandS libraries being represent per long PB read
upperQ	Filter out given percentage of PacBio reads with the highest number of alignments.
theta.param	A list of estimated cell types for each single cell. (rows=clusters, cols=strand states)
pi.param	A vector of estimated sizes of each cluster based on initial hard clustering.
logL.th	Set the difference between objective function from the current and the previous interation for EM algorithm to converge.
theta.constrain	Recalibrate theta values to meet expected distribution of W and C strand across Strand-seq libraries.
store.counts	Logical if to store raw read counts per PB read
HC.input	Filaname where hard clustering results are stored
cellNum	Specifies the number of single cells to be used in clustering

Author(s)

David Porubsky

daewoooo/SaaRclust documentation built on May 28, 2019, 7:50 p.m.