BAIT {contiBAIT} | R Documentation

## BAIT – master function to process strand-seq libraries into BAIT ideograms

### Description

BAIT – master function to process strand-seq libraries into BAIT ideograms

### Usage

    BAIT(path = ".", splitBy = 2e+05, readQual = 10, pairedEnd = TRUE,
      plotBy = "lib", plotName = NULL, chroms = "all", verbose = TRUE)

### Arguments

`path` | String denoting location of Strand-seq bam files (default is ".")
`splitBy` | numeric value of binsize for plotting. default is 200000
`readQual` | Integer dictating the minimal mapping quality required for a read to be accepted. Default is 10.
`pairedEnd` | Whether the bam files being read are in paired end format. Default is TRUE. Note,
`plotBy` | Whether to plot by library ('lib') or chromosome ('chr')
`plotName` | character which determines file name to be saved. Default is to open an R plot from the terminal
`chroms` | vector of chromosome number to prevent contig plotting. eg for humans use 1:24. Default is 'all'
`verbose` | prints messages to the terminal (default is TRUE)

### Value

ideogram plots

### Examples

    ## Not run:

    #Not run because this takes a minute or two:
    bamPath=file.path(system.file(package='contiBAIT'), 'extdata')

    BAIT(bamPath, pairedEnd = FALSE) #our example data is single-end

    ## End(Not run)

[Package contiBAIT version 1.10.1 Index]