runSaaRclust: Wrapper function to run saarclust pipeline.

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.

Usage

runSaaRclust(inputfolder = NULL, outputfolder = "SaaRclust_results",
  num.clusters = 54, EM.iter = 100, alpha = 0.01, minLib = 10,
  upperQ = 0.95, logL.th = 1, theta.constrain = FALSE,
  store.counts = FALSE, store.bestAlign = TRUE,
  numAlignments = 30000, HC.only = TRUE, verbose = TRUE,
  cellNum = NULL, log.scale = FALSE)

Arguments

inputfolder	A folder name where minimap files are stored.
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.
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
store.bestAlign	Store best alignements in RData object.
numAlignments	Required number of best PBvsSS alignmnets to selest for hard clustering.
HC.only	Perform only hard clustering and skip the rest of the pipeline.
verbose	Set to TRUE to print function messages.
cellNum	specifies the number of single cells to be used in clustering
HC.input	Filaname where hard clustering results are stored

Author(s)

David Porubsky, Maryam Ghareghani

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