highlightAssemblyErrors {contiBAIT} | R Documentation

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

### Description

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

### Usage

    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)

[Package contiBAIT version 1.20.0 Index]