filterIntbias: Method filterIntbias

In InesdeSantiago/BaalChIP: BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

Description

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

samplesheet <- system.file("test", "exampleChIP.tsv", package = "BaalChIP")  
hets <- c("MCF7"= system.file("test", "MCF7_hetSNP.txt", package = "BaalChIP"), 
         "GM12891"= system.file("test", "GM12891_hetSNP.txt", package = "BaalChIP"))
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)

InesdeSantiago/BaalChIP documentation built on March 4, 2021, 12:54 a.m.