highlightAssemblyErrors: highlightAssemblyErrors - Master function to identify...

Description Usage Arguments Value

View source: R/highlightAssemblyErrors.R

Description

highlightAssemblyErrors – Master function to identify misorientations and chimeras in the assembly

Usage

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highlightAssemblyErrors(path, splitBy = 1e+06, cluster = 1,
  clusterParam = NULL, pairedEnd = TRUE, qual = 10, gapFile = NULL,
  verbose = TRUE)

Arguments

path

String denoting location of Strand-seq bam files

splitBy

integer determining the average size contigs should be split by

cluster

Number of times to recluster and take the consensus of. If NULL, clustering is run only once.

clusterParam

optional BiocParallelParam specifying cluster to use for parallel execution. When NULL, execution will be serial.

pairedEnd

Whether the bam files being read are in paired end format. Default is TRUE. Note,

qual

Mapping quality threshold. Default is 1

gapFile

A GRanges object consisting of start and end locations of assembly gaps (defaul it NULL)

verbose

prints messages to the terminal (default is TRUE)

Value

a directional ChrTable object that can be used in downstream functions (strandSeqFreqTable)


contiBAIT documentation built on Nov. 8, 2020, 5:49 p.m.