diff --git a/DESCRIPTION b/DESCRIPTION
index 63e24ad6..d9c42287 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -63,4 +63,4 @@ biocViews: CopyNumberVariation, Software, Sequencing,
     VariantAnnotation, VariantDetection, Coverage, ImmunoOncology
 NeedsCompilation: no
 ByteCompile: yes
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.0
diff --git a/man/calculateBamCoverageByInterval.Rd b/man/calculateBamCoverageByInterval.Rd
index 75965e27..7d62e7a1 100644
--- a/man/calculateBamCoverageByInterval.Rd
+++ b/man/calculateBamCoverageByInterval.Rd
@@ -4,9 +4,14 @@
 \alias{calculateBamCoverageByInterval}
 \title{Function to calculate coverage from BAM file}
 \usage{
-calculateBamCoverageByInterval(bam.file, interval.file,
-  output.file = NULL, index.file = bam.file, keep.duplicates = FALSE,
-  ...)
+calculateBamCoverageByInterval(
+  bam.file,
+  interval.file,
+  output.file = NULL,
+  index.file = bam.file,
+  keep.duplicates = FALSE,
+  ...
+)
 }
 \arguments{
 \item{bam.file}{Filename of a BAM file.}
diff --git a/man/calculateIntervalWeights.Rd b/man/calculateIntervalWeights.Rd
index 66e43612..e6677105 100644
--- a/man/calculateIntervalWeights.Rd
+++ b/man/calculateIntervalWeights.Rd
@@ -4,8 +4,13 @@
 \alias{calculateIntervalWeights}
 \title{Calculate interval weights}
 \usage{
-calculateIntervalWeights(normalDB, interval.weight.file = NULL,
-  top.quantile = 0.7, plot = FALSE, normal.coverage.files = NULL)
+calculateIntervalWeights(
+  normalDB,
+  interval.weight.file = NULL,
+  top.quantile = 0.7,
+  plot = FALSE,
+  normal.coverage.files = NULL
+)
 }
 \arguments{
 \item{normalDB}{Database of normal samples, created with
diff --git a/man/calculateMappingBiasVcf.Rd b/man/calculateMappingBiasVcf.Rd
index dfd7f53d..326f5186 100644
--- a/man/calculateMappingBiasVcf.Rd
+++ b/man/calculateMappingBiasVcf.Rd
@@ -4,9 +4,14 @@
 \alias{calculateMappingBiasVcf}
 \title{Calculate Mapping Bias}
 \usage{
-calculateMappingBiasVcf(normal.panel.vcf.file, min.normals = 2,
-  min.normals.betafit = 7, min.median.coverage.betafit = 5,
-  yieldSize = 5000, genome)
+calculateMappingBiasVcf(
+  normal.panel.vcf.file,
+  min.normals = 2,
+  min.normals.betafit = 7,
+  min.median.coverage.betafit = 5,
+  yieldSize = 5000,
+  genome
+)
 }
 \arguments{
 \item{normal.panel.vcf.file}{Combined VCF file of a panel of normals,
diff --git a/man/calculatePowerDetectSomatic.Rd b/man/calculatePowerDetectSomatic.Rd
index 3567a52f..e722515e 100644
--- a/man/calculatePowerDetectSomatic.Rd
+++ b/man/calculatePowerDetectSomatic.Rd
@@ -4,9 +4,16 @@
 \alias{calculatePowerDetectSomatic}
 \title{Power calculation for detecting somatic mutations}
 \usage{
-calculatePowerDetectSomatic(coverage, f = NULL, purity = NULL,
-  ploidy = NULL, cell.fraction = 1, error = 0.001, fpr = 5e-07,
-  verbose = TRUE)
+calculatePowerDetectSomatic(
+  coverage,
+  f = NULL,
+  purity = NULL,
+  ploidy = NULL,
+  cell.fraction = 1,
+  error = 0.001,
+  fpr = 5e-07,
+  verbose = TRUE
+)
 }
 \arguments{
 \item{coverage}{Mean sequencing coverage.}
diff --git a/man/calculateTangentNormal.Rd b/man/calculateTangentNormal.Rd
index 500ab293..7fa01d8e 100644
--- a/man/calculateTangentNormal.Rd
+++ b/man/calculateTangentNormal.Rd
@@ -4,8 +4,13 @@
 \alias{calculateTangentNormal}
 \title{Calculate tangent normal}
 \usage{
-calculateTangentNormal(tumor.coverage.file, normalDB, num.eigen = 20,
-  ignore.sex = FALSE, sex = NULL)
+calculateTangentNormal(
+  tumor.coverage.file,
+  normalDB,
+  num.eigen = 20,
+  ignore.sex = FALSE,
+  sex = NULL
+)
 }
 \arguments{
 \item{tumor.coverage.file}{Coverage file or data  of a tumor sample.}
diff --git a/man/callAlterations.Rd b/man/callAlterations.Rd
index 0ff0f191..bbb856bc 100644
--- a/man/callAlterations.Rd
+++ b/man/callAlterations.Rd
@@ -4,8 +4,14 @@
 \alias{callAlterations}
 \title{Calling of amplifications and deletions}
 \usage{
-callAlterations(res, id = 1, cutoffs = c(0.5, 6, 7),
-  log.ratio.cutoffs = c(-0.9, 0.9), failed = NULL, all.genes = FALSE)
+callAlterations(
+  res,
+  id = 1,
+  cutoffs = c(0.5, 6, 7),
+  log.ratio.cutoffs = c(-0.9, 0.9),
+  failed = NULL,
+  all.genes = FALSE
+)
 }
 \arguments{
 \item{res}{Return object of the \code{\link{runAbsoluteCN}} function.}
diff --git a/man/callAlterationsFromSegmentation.Rd b/man/callAlterationsFromSegmentation.Rd
index 88997bf7..f11242a4 100644
--- a/man/callAlterationsFromSegmentation.Rd
+++ b/man/callAlterationsFromSegmentation.Rd
@@ -4,9 +4,19 @@
 \alias{callAlterationsFromSegmentation}
 \title{Calling of amplifications and deletions from segmentations}
 \usage{
-callAlterationsFromSegmentation(sampleid, chr, start, end, num.mark = NA,
-  seg.mean, C, interval.file, fun.focal = findFocal,
-  args.focal = list(), ...)
+callAlterationsFromSegmentation(
+  sampleid,
+  chr,
+  start,
+  end,
+  num.mark = NA,
+  seg.mean,
+  C,
+  interval.file,
+  fun.focal = findFocal,
+  args.focal = list(),
+  ...
+)
 }
 \arguments{
 \item{sampleid}{The sampleid column in the segmentation file.}
diff --git a/man/callAmplificationsInLowPurity.Rd b/man/callAmplificationsInLowPurity.Rd
index 21a86b01..51740c74 100644
--- a/man/callAmplificationsInLowPurity.Rd
+++ b/man/callAmplificationsInLowPurity.Rd
@@ -4,9 +4,15 @@
 \alias{callAmplificationsInLowPurity}
 \title{Calling of amplifications in low purity samples}
 \usage{
-callAmplificationsInLowPurity(res, normalDB, pvalue.cutoff = 0.001,
-  percentile.cutoff = 90, min.width = 3, all.genes = FALSE,
-  purity = NULL)
+callAmplificationsInLowPurity(
+  res,
+  normalDB,
+  pvalue.cutoff = 0.001,
+  percentile.cutoff = 90,
+  min.width = 3,
+  all.genes = FALSE,
+  purity = NULL
+)
 }
 \arguments{
 \item{res}{Return object of the \code{\link{runAbsoluteCN}} function.}
diff --git a/man/callCIN.Rd b/man/callCIN.Rd
index fec4c411..66abc2bf 100644
--- a/man/callCIN.Rd
+++ b/man/callCIN.Rd
@@ -4,8 +4,12 @@
 \alias{callCIN}
 \title{Call Chromosomal Instability}
 \usage{
-callCIN(res, id = 1, allele.specific = TRUE,
-  reference.state = c("dominant", "normal"))
+callCIN(
+  res,
+  id = 1,
+  allele.specific = TRUE,
+  reference.state = c("dominant", "normal")
+)
 }
 \arguments{
 \item{res}{Return object of the \code{\link{runAbsoluteCN}} function.}
diff --git a/man/callMutationBurden.Rd b/man/callMutationBurden.Rd
index d5e89879..377422c8 100644
--- a/man/callMutationBurden.Rd
+++ b/man/callMutationBurden.Rd
@@ -4,10 +4,17 @@
 \alias{callMutationBurden}
 \title{Call mutation burden}
 \usage{
-callMutationBurden(res, id = 1, remove.flagged = TRUE,
-  min.prior.somatic = 0.1, max.prior.somatic = 1,
-  min.cellfraction = 0, fun.countMutation = function(vcf) width(vcf) ==
-  1, callable = NULL, exclude = NULL)
+callMutationBurden(
+  res,
+  id = 1,
+  remove.flagged = TRUE,
+  min.prior.somatic = 0.1,
+  max.prior.somatic = 1,
+  min.cellfraction = 0,
+  fun.countMutation = function(vcf) width(vcf) == 1,
+  callable = NULL,
+  exclude = NULL
+)
 }
 \arguments{
 \item{res}{Return object of the \code{\link{runAbsoluteCN}} function.}
diff --git a/man/correctCoverageBias.Rd b/man/correctCoverageBias.Rd
index 480b0f5b..89731620 100644
--- a/man/correctCoverageBias.Rd
+++ b/man/correctCoverageBias.Rd
@@ -4,8 +4,14 @@
 \alias{correctCoverageBias}
 \title{Correct for library-specific coverage biases}
 \usage{
-correctCoverageBias(coverage.file, interval.file, output.file = NULL,
-  plot.bias = FALSE, plot.max.density = 50000, output.qc.file = NULL)
+correctCoverageBias(
+  coverage.file,
+  interval.file,
+  output.file = NULL,
+  plot.bias = FALSE,
+  plot.max.density = 50000,
+  output.qc.file = NULL
+)
 }
 \arguments{
 \item{coverage.file}{Coverage file or coverage data parsed with the
diff --git a/man/createCurationFile.Rd b/man/createCurationFile.Rd
index a5296fb1..5f9ca721 100644
--- a/man/createCurationFile.Rd
+++ b/man/createCurationFile.Rd
@@ -4,8 +4,11 @@
 \alias{createCurationFile}
 \title{Create file to curate PureCN results}
 \usage{
-createCurationFile(file.rds, overwrite.uncurated = TRUE,
-  overwrite.curated = FALSE)
+createCurationFile(
+  file.rds,
+  overwrite.uncurated = TRUE,
+  overwrite.curated = FALSE
+)
 }
 \arguments{
 \item{file.rds}{Output of the \code{\link{runAbsoluteCN}} function,
diff --git a/man/createNormalDatabase.Rd b/man/createNormalDatabase.Rd
index afc20ed7..058bdb44 100644
--- a/man/createNormalDatabase.Rd
+++ b/man/createNormalDatabase.Rd
@@ -4,9 +4,16 @@
 \alias{createNormalDatabase}
 \title{Create database of normal samples}
 \usage{
-createNormalDatabase(normal.coverage.files, sex = NULL,
-  coverage.outliers = c(0.25, 4), min.coverage = 0.25,
-  max.missing = 0.03, low.coverage = 15, plot = FALSE, ...)
+createNormalDatabase(
+  normal.coverage.files,
+  sex = NULL,
+  coverage.outliers = c(0.25, 4),
+  min.coverage = 0.25,
+  max.missing = 0.03,
+  low.coverage = 15,
+  plot = FALSE,
+  ...
+)
 }
 \arguments{
 \item{normal.coverage.files}{Vector with file names pointing to 
diff --git a/man/filterIntervals.Rd b/man/filterIntervals.Rd
index e38204d0..8373357b 100644
--- a/man/filterIntervals.Rd
+++ b/man/filterIntervals.Rd
@@ -4,9 +4,16 @@
 \alias{filterIntervals}
 \title{Remove low quality intervals}
 \usage{
-filterIntervals(normal, tumor, log.ratio, seg.file,
-  filter.lowhigh.gc = 0.001, min.coverage = 15,
-  min.targeted.base = 5, normalDB = NULL)
+filterIntervals(
+  normal,
+  tumor,
+  log.ratio,
+  seg.file,
+  filter.lowhigh.gc = 0.001,
+  min.coverage = 15,
+  min.targeted.base = 5,
+  normalDB = NULL
+)
 }
 \arguments{
 \item{normal}{Coverage data for normal sample.}
diff --git a/man/filterVcfBasic.Rd b/man/filterVcfBasic.Rd
index 1da58c61..b1a3f895 100644
--- a/man/filterVcfBasic.Rd
+++ b/man/filterVcfBasic.Rd
@@ -4,13 +4,23 @@
 \alias{filterVcfBasic}
 \title{Basic VCF filter function}
 \usage{
-filterVcfBasic(vcf, tumor.id.in.vcf = NULL, use.somatic.status = TRUE,
-  snp.blacklist = NULL, af.range = c(0.03, 0.97),
-  contamination.range = c(0.01, 0.075), min.coverage = 15,
-  min.base.quality = 25, min.supporting.reads = NULL, error = 0.001,
-  target.granges = NULL, remove.off.target.snvs = TRUE,
-  model.homozygous = FALSE, interval.padding = 50,
-  DB.info.flag = "DB")
+filterVcfBasic(
+  vcf,
+  tumor.id.in.vcf = NULL,
+  use.somatic.status = TRUE,
+  snp.blacklist = NULL,
+  af.range = c(0.03, 0.97),
+  contamination.range = c(0.01, 0.075),
+  min.coverage = 15,
+  min.base.quality = 25,
+  min.supporting.reads = NULL,
+  error = 0.001,
+  target.granges = NULL,
+  remove.off.target.snvs = TRUE,
+  model.homozygous = FALSE,
+  interval.padding = 50,
+  DB.info.flag = "DB"
+)
 }
 \arguments{
 \item{vcf}{\code{CollapsedVCF} object, read in with the \code{readVcf}
diff --git a/man/filterVcfMuTect.Rd b/man/filterVcfMuTect.Rd
index 7b69b1e3..d165348b 100644
--- a/man/filterVcfMuTect.Rd
+++ b/man/filterVcfMuTect.Rd
@@ -4,11 +4,15 @@
 \alias{filterVcfMuTect}
 \title{Filter VCF MuTect}
 \usage{
-filterVcfMuTect(vcf, tumor.id.in.vcf = NULL, stats.file = NULL,
-  ignore = c("clustered_read_position", "fstar_tumor_lod",
-  "nearby_gap_events", "poor_mapping_region_alternate_allele_mapq",
-  "poor_mapping_region_mapq0", "possible_contamination", "strand_artifact",
-  "seen_in_panel_of_normals"), ...)
+filterVcfMuTect(
+  vcf,
+  tumor.id.in.vcf = NULL,
+  stats.file = NULL,
+  ignore = c("clustered_read_position", "fstar_tumor_lod", "nearby_gap_events",
+    "poor_mapping_region_alternate_allele_mapq", "poor_mapping_region_mapq0",
+    "possible_contamination", "strand_artifact", "seen_in_panel_of_normals"),
+  ...
+)
 }
 \arguments{
 \item{vcf}{\code{CollapsedVCF} object, read in with the \code{readVcf}
diff --git a/man/filterVcfMuTect2.Rd b/man/filterVcfMuTect2.Rd
index c6e6e145..ab88998e 100644
--- a/man/filterVcfMuTect2.Rd
+++ b/man/filterVcfMuTect2.Rd
@@ -4,10 +4,14 @@
 \alias{filterVcfMuTect2}
 \title{Filter VCF MuTect2}
 \usage{
-filterVcfMuTect2(vcf, tumor.id.in.vcf = NULL,
-  ignore = c("clustered_events", "t_lod", "str_contraction",
-  "read_position", "fragment_length", "multiallelic", "clipping",
-  "strand_artifact"), ...)
+filterVcfMuTect2(
+  vcf,
+  tumor.id.in.vcf = NULL,
+  ignore = c("clustered_events", "t_lod", "str_contraction", "read_position",
+    "position", "fragment_length", "multiallelic", "clipping", "strand_artifact",
+    "strand_bias", "slippage", "weak_evidence", "orientation", "haplotype"),
+  ...
+)
 }
 \arguments{
 \item{vcf}{\code{CollapsedVCF} object, read in with the \code{readVcf}
diff --git a/man/getSexFromCoverage.Rd b/man/getSexFromCoverage.Rd
index 9f5baba0..02acf213 100644
--- a/man/getSexFromCoverage.Rd
+++ b/man/getSexFromCoverage.Rd
@@ -4,8 +4,12 @@
 \alias{getSexFromCoverage}
 \title{Get sample sex from coverage}
 \usage{
-getSexFromCoverage(coverage.file, min.ratio = 25, min.ratio.na = 20,
-  remove.outliers = TRUE)
+getSexFromCoverage(
+  coverage.file,
+  min.ratio = 25,
+  min.ratio.na = 20,
+  remove.outliers = TRUE
+)
 }
 \arguments{
 \item{coverage.file}{Coverage file or data read with
diff --git a/man/getSexFromVcf.Rd b/man/getSexFromVcf.Rd
index 63a3536c..3b8ead6c 100644
--- a/man/getSexFromVcf.Rd
+++ b/man/getSexFromVcf.Rd
@@ -4,9 +4,17 @@
 \alias{getSexFromVcf}
 \title{Get sample sex from a VCF file}
 \usage{
-getSexFromVcf(vcf, tumor.id.in.vcf = NULL, min.or = 4,
-  min.or.na = 2.5, max.pv = 0.001, homozygous.cutoff = 0.95,
-  af.cutoff = 0.2, min.coverage = 15, use.somatic.status = TRUE)
+getSexFromVcf(
+  vcf,
+  tumor.id.in.vcf = NULL,
+  min.or = 4,
+  min.or.na = 2.5,
+  max.pv = 0.001,
+  homozygous.cutoff = 0.95,
+  af.cutoff = 0.2,
+  min.coverage = 15,
+  use.somatic.status = TRUE
+)
 }
 \arguments{
 \item{vcf}{CollapsedVCF object, read in with the \code{readVcf} function
diff --git a/man/plotAbs.Rd b/man/plotAbs.Rd
index c990b27f..62e44630 100644
--- a/man/plotAbs.Rd
+++ b/man/plotAbs.Rd
@@ -4,12 +4,23 @@
 \alias{plotAbs}
 \title{Plots for analyzing PureCN solutions}
 \usage{
-plotAbs(res, id = 1, type = c("hist", "overview", "BAF", "AF", "all"),
-  chr = NULL, germline.only = TRUE, show.contour = FALSE,
-  purity = NULL, ploidy = NULL, alpha = TRUE,
+plotAbs(
+  res,
+  id = 1,
+  type = c("hist", "overview", "BAF", "AF", "all"),
+  chr = NULL,
+  germline.only = TRUE,
+  show.contour = FALSE,
+  purity = NULL,
+  ploidy = NULL,
+  alpha = TRUE,
   show.segment.means = c("SNV", "segments", "both"),
-  max.mapping.bias = 0.8, palette.name = "Paired",
-  col.snps = "#2b6391", col.chr.shading = "#f0f0f0", ...)
+  max.mapping.bias = 0.8,
+  palette.name = "Paired",
+  col.snps = "#2b6391",
+  col.chr.shading = "#f0f0f0",
+  ...
+)
 }
 \arguments{
 \item{res}{Return object of the \code{\link{runAbsoluteCN}} function.}
diff --git a/man/predictSomatic.Rd b/man/predictSomatic.Rd
index bb6f5252..243f71ef 100644
--- a/man/predictSomatic.Rd
+++ b/man/predictSomatic.Rd
@@ -4,8 +4,7 @@
 \alias{predictSomatic}
 \title{Predict germline vs. somatic status}
 \usage{
-predictSomatic(res, id = 1, return.vcf = FALSE,
-  vcf.field.prefix = "")
+predictSomatic(res, id = 1, return.vcf = FALSE, vcf.field.prefix = "")
 }
 \arguments{
 \item{res}{Return object of the \code{\link{runAbsoluteCN}} function.}
diff --git a/man/preprocessIntervals.Rd b/man/preprocessIntervals.Rd
index af6cf0e3..3d855d4c 100644
--- a/man/preprocessIntervals.Rd
+++ b/man/preprocessIntervals.Rd
@@ -4,14 +4,24 @@
 \alias{preprocessIntervals}
 \title{Preprocess intervals}
 \usage{
-preprocessIntervals(interval.file, reference.file, output.file = NULL,
-  off.target = FALSE, average.target.width = 400,
-  min.target.width = 100, min.off.target.width = 20000,
-  average.off.target.width = 2e+05, off.target.padding = -500,
-  mappability = NULL, min.mappability = c(0.5, 0.1, 0.7),
-  reptiming = NULL, average.reptiming.width = 1e+05, exclude = NULL,
+preprocessIntervals(
+  interval.file,
+  reference.file,
+  output.file = NULL,
+  off.target = FALSE,
+  average.target.width = 400,
+  min.target.width = 100,
+  min.off.target.width = 20000,
+  average.off.target.width = 2e+05,
+  off.target.padding = -500,
+  mappability = NULL,
+  min.mappability = c(0.5, 0.1, 0.7),
+  reptiming = NULL,
+  average.reptiming.width = 1e+05,
+  exclude = NULL,
   off.target.seqlevels = c("targeted", "all"),
-  small.targets = c("resize", "drop"))
+  small.targets = c("resize", "drop")
+)
 }
 \arguments{
 \item{interval.file}{File specifying the intervals. Interval is expected in
diff --git a/man/processMultipleSamples.Rd b/man/processMultipleSamples.Rd
index 4ebdb8f9..52a3f4fb 100644
--- a/man/processMultipleSamples.Rd
+++ b/man/processMultipleSamples.Rd
@@ -4,10 +4,21 @@
 \alias{processMultipleSamples}
 \title{Multi sample normalization and segmentation}
 \usage{
-processMultipleSamples(tumor.coverage.files, sampleids, normalDB,
-  num.eigen = 20, genome, plot.cnv = TRUE, w = NULL,
-  interval.weight.file = NULL, min.interval.weight = 1/3,
-  max.segments = NULL, chr.hash = NULL, centromeres = NULL, ...)
+processMultipleSamples(
+  tumor.coverage.files,
+  sampleids,
+  normalDB,
+  num.eigen = 20,
+  genome,
+  plot.cnv = TRUE,
+  w = NULL,
+  interval.weight.file = NULL,
+  min.interval.weight = 1/3,
+  max.segments = NULL,
+  chr.hash = NULL,
+  centromeres = NULL,
+  ...
+)
 }
 \arguments{
 \item{tumor.coverage.files}{Coverage data for tumor samples.}
diff --git a/man/readCurationFile.Rd b/man/readCurationFile.Rd
index 1935ed26..744fe89e 100644
--- a/man/readCurationFile.Rd
+++ b/man/readCurationFile.Rd
@@ -4,9 +4,14 @@
 \alias{readCurationFile}
 \title{Read curation file}
 \usage{
-readCurationFile(file.rds, file.curation = gsub(".rds$", ".csv",
-  file.rds), remove.failed = FALSE, report.best.only = FALSE,
-  min.ploidy = NULL, max.ploidy = NULL)
+readCurationFile(
+  file.rds,
+  file.curation = gsub(".rds$", ".csv", file.rds),
+  remove.failed = FALSE,
+  report.best.only = FALSE,
+  min.ploidy = NULL,
+  max.ploidy = NULL
+)
 }
 \arguments{
 \item{file.rds}{Output of the \code{\link{runAbsoluteCN}} function,
diff --git a/man/readSegmentationFile.Rd b/man/readSegmentationFile.Rd
index a18bd6c3..3d05a41a 100644
--- a/man/readSegmentationFile.Rd
+++ b/man/readSegmentationFile.Rd
@@ -4,8 +4,14 @@
 \alias{readSegmentationFile}
 \title{Read file containing segmentations}
 \usage{
-readSegmentationFile(seg.file, sampleid, model.homozygous = FALSE,
-  format, zero = FALSE, verbose = TRUE)
+readSegmentationFile(
+  seg.file,
+  sampleid,
+  model.homozygous = FALSE,
+  format,
+  zero = FALSE,
+  verbose = TRUE
+)
 }
 \arguments{
 \item{seg.file}{File with segmentation}
diff --git a/man/runAbsoluteCN.Rd b/man/runAbsoluteCN.Rd
index b183c47e..20442a3c 100644
--- a/man/runAbsoluteCN.Rd
+++ b/man/runAbsoluteCN.Rd
@@ -4,32 +4,70 @@
 \alias{runAbsoluteCN}
 \title{Run PureCN implementation of ABSOLUTE}
 \usage{
-runAbsoluteCN(normal.coverage.file = NULL, tumor.coverage.file = NULL,
-  log.ratio = NULL, seg.file = NULL, seg.file.sdev = 0.4,
-  vcf.file = NULL, normalDB = NULL, genome, centromeres = NULL,
-  sex = c("?", "F", "M", "diploid"), fun.filterVcf = filterVcfMuTect,
-  args.filterVcf = list(), fun.setPriorVcf = setPriorVcf,
-  args.setPriorVcf = list(), fun.setMappingBiasVcf = setMappingBiasVcf,
+runAbsoluteCN(
+  normal.coverage.file = NULL,
+  tumor.coverage.file = NULL,
+  log.ratio = NULL,
+  seg.file = NULL,
+  seg.file.sdev = 0.4,
+  vcf.file = NULL,
+  normalDB = NULL,
+  genome,
+  centromeres = NULL,
+  sex = c("?", "F", "M", "diploid"),
+  fun.filterVcf = filterVcfMuTect,
+  args.filterVcf = list(),
+  fun.setPriorVcf = setPriorVcf,
+  args.setPriorVcf = list(),
+  fun.setMappingBiasVcf = setMappingBiasVcf,
   args.setMappingBiasVcf = list(),
-  fun.filterIntervals = filterIntervals, args.filterIntervals = list(),
-  fun.segmentation = segmentationCBS, args.segmentation = list(),
-  fun.focal = findFocal, args.focal = list(), sampleid = NULL,
-  min.ploidy = 1, max.ploidy = 6, test.num.copy = 0:7,
-  test.purity = seq(0.15, 0.95, by = 0.01), prior.purity = NULL,
-  prior.K = 0.999, prior.contamination = 0.01,
-  max.candidate.solutions = 20, candidates = NULL, min.coverage = 15,
-  max.coverage.vcf = 300, max.non.clonal = 0.2,
-  max.homozygous.loss = c(0.05, 1e+07), non.clonal.M = 1/3,
-  max.mapping.bias = 0.8, max.pon = 3, iterations = 30,
-  min.variants.segment = 5, log.ratio.calibration = 0.1,
-  smooth.log.ratio = TRUE, model.homozygous = FALSE, error = 0.001,
-  interval.file = NULL, max.dropout = c(0.95, 1.1),
-  min.logr.sdev = 0.15, max.logr.sdev = 0.6, max.segments = 300,
-  min.gof = 0.8, plot.cnv = TRUE, cosmic.vcf.file = NULL,
-  DB.info.flag = "DB", POPAF.info.field = "POP_AF",
-  min.pop.af = 0.001, model = c("beta", "betabin"),
-  post.optimize = FALSE, speedup.heuristics = 2, BPPARAM = NULL,
-  log.file = NULL, verbose = TRUE)
+  fun.filterIntervals = filterIntervals,
+  args.filterIntervals = list(),
+  fun.segmentation = segmentationCBS,
+  args.segmentation = list(),
+  fun.focal = findFocal,
+  args.focal = list(),
+  sampleid = NULL,
+  min.ploidy = 1,
+  max.ploidy = 6,
+  test.num.copy = 0:7,
+  test.purity = seq(0.15, 0.95, by = 0.01),
+  prior.purity = NULL,
+  prior.K = 0.999,
+  prior.contamination = 0.01,
+  max.candidate.solutions = 20,
+  candidates = NULL,
+  min.coverage = 15,
+  max.coverage.vcf = 300,
+  max.non.clonal = 0.2,
+  max.homozygous.loss = c(0.05, 1e+07),
+  non.clonal.M = 1/3,
+  max.mapping.bias = 0.8,
+  max.pon = 3,
+  iterations = 30,
+  min.variants.segment = 5,
+  log.ratio.calibration = 0.1,
+  smooth.log.ratio = TRUE,
+  model.homozygous = FALSE,
+  error = 0.001,
+  interval.file = NULL,
+  max.dropout = c(0.95, 1.1),
+  min.logr.sdev = 0.15,
+  max.logr.sdev = 0.6,
+  max.segments = 300,
+  min.gof = 0.8,
+  plot.cnv = TRUE,
+  cosmic.vcf.file = NULL,
+  DB.info.flag = "DB",
+  POPAF.info.field = "POP_AF",
+  min.pop.af = 0.001,
+  model = c("beta", "betabin"),
+  post.optimize = FALSE,
+  speedup.heuristics = 2,
+  BPPARAM = NULL,
+  log.file = NULL,
+  verbose = TRUE
+)
 }
 \arguments{
 \item{normal.coverage.file}{Coverage file of normal control (optional
diff --git a/man/segmentationCBS.Rd b/man/segmentationCBS.Rd
index a634ae45..9a184a81 100644
--- a/man/segmentationCBS.Rd
+++ b/man/segmentationCBS.Rd
@@ -4,12 +4,26 @@
 \alias{segmentationCBS}
 \title{CBS segmentation}
 \usage{
-segmentationCBS(normal, tumor, log.ratio, seg, plot.cnv, sampleid,
-  interval.weight.file = NULL, weight.flag.pvalue = 0.01,
-  alpha = 0.005, undo.SD = NULL, vcf = NULL, tumor.id.in.vcf = 1,
-  normal.id.in.vcf = NULL, max.segments = NULL,
-  prune.hclust.h = NULL, prune.hclust.method = "ward.D",
-  chr.hash = NULL, centromeres = NULL)
+segmentationCBS(
+  normal,
+  tumor,
+  log.ratio,
+  seg,
+  plot.cnv,
+  sampleid,
+  interval.weight.file = NULL,
+  weight.flag.pvalue = 0.01,
+  alpha = 0.005,
+  undo.SD = NULL,
+  vcf = NULL,
+  tumor.id.in.vcf = 1,
+  normal.id.in.vcf = NULL,
+  max.segments = NULL,
+  prune.hclust.h = NULL,
+  prune.hclust.method = "ward.D",
+  chr.hash = NULL,
+  centromeres = NULL
+)
 }
 \arguments{
 \item{normal}{Coverage data for normal sample.}
diff --git a/man/segmentationHclust.Rd b/man/segmentationHclust.Rd
index 63b814a3..7808a9e7 100644
--- a/man/segmentationHclust.Rd
+++ b/man/segmentationHclust.Rd
@@ -4,9 +4,16 @@
 \alias{segmentationHclust}
 \title{Minimal segmentation function}
 \usage{
-segmentationHclust(seg, vcf = NULL, tumor.id.in.vcf = 1,
-  normal.id.in.vcf = NULL, prune.hclust.h = NULL,
-  prune.hclust.method = "ward.D", chr.hash = NULL, ...)
+segmentationHclust(
+  seg,
+  vcf = NULL,
+  tumor.id.in.vcf = 1,
+  normal.id.in.vcf = NULL,
+  prune.hclust.h = NULL,
+  prune.hclust.method = "ward.D",
+  chr.hash = NULL,
+  ...
+)
 }
 \arguments{
 \item{seg}{If segmentation was provided by the user, this data structure
diff --git a/man/segmentationPSCBS.Rd b/man/segmentationPSCBS.Rd
index 3172cc62..289e0d76 100644
--- a/man/segmentationPSCBS.Rd
+++ b/man/segmentationPSCBS.Rd
@@ -4,13 +4,29 @@
 \alias{segmentationPSCBS}
 \title{PSCBS segmentation}
 \usage{
-segmentationPSCBS(normal, tumor, log.ratio, seg, plot.cnv, sampleid,
-  interval.weight.file = NULL, weight.flag.pvalue = 0.01,
-  alpha = 0.005, undo.SD = NULL, flavor = "tcn&dh", tauA = 0.03,
-  vcf = NULL, tumor.id.in.vcf = 1, normal.id.in.vcf = NULL,
-  max.segments = NULL, prune.hclust.h = NULL,
-  prune.hclust.method = "ward.D", chr.hash = NULL,
-  centromeres = NULL, ...)
+segmentationPSCBS(
+  normal,
+  tumor,
+  log.ratio,
+  seg,
+  plot.cnv,
+  sampleid,
+  interval.weight.file = NULL,
+  weight.flag.pvalue = 0.01,
+  alpha = 0.005,
+  undo.SD = NULL,
+  flavor = "tcn&dh",
+  tauA = 0.03,
+  vcf = NULL,
+  tumor.id.in.vcf = 1,
+  normal.id.in.vcf = NULL,
+  max.segments = NULL,
+  prune.hclust.h = NULL,
+  prune.hclust.method = "ward.D",
+  chr.hash = NULL,
+  centromeres = NULL,
+  ...
+)
 }
 \arguments{
 \item{normal}{Coverage data for normal sample.}
diff --git a/man/setMappingBiasVcf.Rd b/man/setMappingBiasVcf.Rd
index e6db0fe1..416a77ff 100644
--- a/man/setMappingBiasVcf.Rd
+++ b/man/setMappingBiasVcf.Rd
@@ -4,9 +4,15 @@
 \alias{setMappingBiasVcf}
 \title{Set Mapping Bias VCF}
 \usage{
-setMappingBiasVcf(vcf, tumor.id.in.vcf = NULL,
-  mapping.bias.file = NULL, normal.panel.vcf.file = NULL,
-  min.normals = 2, smooth = TRUE, smooth.n = 5)
+setMappingBiasVcf(
+  vcf,
+  tumor.id.in.vcf = NULL,
+  mapping.bias.file = NULL,
+  normal.panel.vcf.file = NULL,
+  min.normals = 2,
+  smooth = TRUE,
+  smooth.n = 5
+)
 }
 \arguments{
 \item{vcf}{\code{CollapsedVCF} object, read in with the \code{readVcf}
diff --git a/man/setPriorVcf.Rd b/man/setPriorVcf.Rd
index a961537c..bf950990 100644
--- a/man/setPriorVcf.Rd
+++ b/man/setPriorVcf.Rd
@@ -4,8 +4,13 @@
 \alias{setPriorVcf}
 \title{Set Somatic Prior VCF}
 \usage{
-setPriorVcf(vcf, prior.somatic = c(0.5, 5e-04, 0.999, 1e-04, 0.995, 0.5),
-  tumor.id.in.vcf = NULL, min.cosmic.cnt = 6, DB.info.flag = "DB")
+setPriorVcf(
+  vcf,
+  prior.somatic = c(0.5, 5e-04, 0.999, 1e-04, 0.995, 0.5),
+  tumor.id.in.vcf = NULL,
+  min.cosmic.cnt = 6,
+  DB.info.flag = "DB"
+)
 }
 \arguments{
 \item{vcf}{\code{CollapsedVCF} object, read in with the \code{readVcf}