filterIntbias {BaalChIP} | R Documentation |
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.
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)
.Object |
An object of the |
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 |
An updated BaalChIP
object with the slot alleleCounts
containing a list of GRanges objects that pass filters.
Ines de Santiago
BaalChIP.get
, plotQC
, summaryQC
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)