filterIntbias {BaalChIP} | R Documentation

## Method filterIntbias

### Description

Method filterIntbias

Filters the data frame available within a `BaalChIP` object (slot `alleleCounts`). This filter performs simulations of reads of the same length as the original ChIP-seq reads, aligns the simulated reads to the genome, calculates the allelic ratios for each variant and finally ignores those variants for which the allelic ratio (REF/TOTAL) is different than 0.5.

### Usage

    filterIntbias(.Object, simul_output = NULL, tmpfile_prefix = NULL,
      simulation_script = "local", alignmentSimulArgs = NULL,
      skipScriptRun = FALSE, verbose = TRUE)

    ## S4 method for signature 'BaalChIP'
    filterIntbias(.Object, simul_output = NULL,
      tmpfile_prefix = NULL, simulation_script = "local",
      alignmentSimulArgs = NULL, skipScriptRun = FALSE, verbose = TRUE)

### Arguments

`.Object` | An object of the `BaalChIP` class.
`simul_output` | a non-empty character vector giving the directory of where to save the FASTQ and BAM files generated by the function. If NULL, a random directory under the current working directory will be generated.
`tmpfile_prefix` | an optional character vector giving the initial part of the name of the FASTQ and BAM files generated by the function. If NULL, a random name will be generated.
`simulation_script` | the file path for simulation script containing the instructions of simulation and alignment commands. If NULL, the default simulation script distributed with BaalChIP ('extra/simulation_run.sh') will be used.
`alignmentSimulArgs` | a character vector with arguments to the simulation script. If NULL no arguments are passed.
`skipScriptRun` | a logical value indicating if simulation BAM files should not be generated. If TRUE BaalChIP will look for the BAM files in the 'simul_output/temp_prefix' (default is FALSE).
`verbose` | logical. If TRUE reports extra information on the process

### Value

An updated `BaalChIP` object with the slot `alleleCounts` containing a list of GRanges objects that pass filters.

### Author(s)

Ines de Santiago

### See Also

`BaalChIP.get`, `plotQC`, `summaryQC`

### Examples

    setwd(system.file('test',package='BaalChIP'))
    samplesheet <- 'exampleChIP.tsv'
    hets <- c('MCF7'='MCF7_hetSNP.txt', 'GM12891'='GM12891_hetSNP.txt')
    res <- BaalChIP(samplesheet=samplesheet, hets=hets)
    res <- alleleCounts(res, min_base_quality=10, min_mapq=15)
    skipScriptRun=TRUE #For demonstration purposes only (read details in vignette)
    res <- filterIntbias(res,
          simul_output=system.file('test/simuloutput',package='BaalChIP'),
          tmpfile_prefix='c67c6ec6c433', skipScriptRun=TRUE)

    #check results
    plotSimul(res)
    summaryQC(res)

[Package BaalChIP version 1.12.0 Index]