Upgrade to v 2.2.5

DESCRIPTION

@@ -3,7 +3,7 @@ Maintainer: Stefan Dentro <sd11@sanger.ac.uk>
 License: GPL-3
 Type: Package
 Title: Battenberg subclonal copy number caller
-Version: 2.2.4
+Version: 2.2.5
 Authors@R: c(person("David", "Wedge", role=c("aut"), email="dw9@sanger.ac.uk"),
     person("Peter", "Van Loo", role=c("aut")),
     person("Stefan","Dentro", email="sd11@sanger.ac.uk", role=c("aut", "cre")),

NAMESPACE

@@ -28,5 +28,6 @@ export(segment.baf.phased.sv)
 export(squaresplot)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(readr,read_table)
-import(ASCAT)
 import(ggplot2)
+import(ASCAT)
+

man/callSubclones.Rd

@@ -8,7 +8,7 @@ callSubclones(sample.name, baf.segmented.file, logr.file, rho.psi.file,
   output.file, output.figures.prefix, output.gw.figures.prefix, chr_names,
   masking_output_file, max_allowed_state = 250, sv_breakpoints_file = NULL,
   gamma = 1, segmentation.gamma = NA, siglevel = 0.05, maxdist = 0.01,
-  noperms = 1000, seed = as.integer(Sys.time()))
+  noperms = 1000, seed = as.integer(Sys.time()), calc_seg_baf_option = 1)
 }
 \arguments{
 \item{sample.name}{Name of the sample, used in figures}
@@ -42,6 +42,8 @@ callSubclones(sample.name, baf.segmented.file, logr.file, rho.psi.file,
 \item{maxdist}{Slack in BAF space to allow a segment to be off it's optimum before becoming significant. A segment becomes significant very quickly when a breakpoint is missed, this parameter alleviates the effect (Default 0.01)}
 
 \item{noperms}{The number of permutations to be run when bootstrapping the confidence intervals on the copy number state of each segment (Default 1000)}
+
+\item{calc_seg_baf_option}{Various options to recalculate the BAF of a segment. Options are: 1 - median, 2 - mean. (Default: 1)}
 }
 \description{
 This function fits a subclonal copy number profile where a clonal profile is unlikely.

man/segment.baf.phased.Rd

@@ -5,7 +5,7 @@
 \title{Segment the haplotyped and phased data using fastPCF.}
 \usage{
 segment.baf.phased(samplename, inputfile, outputfile, gamma = 10,
-  phasegamma = 3, kmin = 3, phasekmin = 3)
+  phasegamma = 3, kmin = 3, phasekmin = 3, calc_seg_baf_option = 1)
 }
 \arguments{
 \item{samplename}{Name of the sample, which is used to name output figures}
@@ -14,13 +14,15 @@ segment.baf.phased(samplename, inputfile, outputfile, gamma = 10,
 
 \item{outputfile}{String where the segmentation output will be written}
 
-\item{gamma}{The gamma parameter controls the size of the penalty of starting a new segment during segmentation. It is therefore the key parameter for controlling the number of segments (Default 10)}
+\item{gamma}{The gamma parameter controls the size of the penalty of starting a new segment during segmentation. It is therefore the key parameter for controlling the number of segments (Default: 10)}
 
-\item{phasegamma}{Gamma parameter used when correcting phasing mistakes (Default 3)}
+\item{phasegamma}{Gamma parameter used when correcting phasing mistakes (Default: 3)}
 
-\item{kmin}{Kmin represents the minimum number of probes/SNPs that a segment should consist of (Default 3)}
+\item{kmin}{Kmin represents the minimum number of probes/SNPs that a segment should consist of (Default: 3)}
 
-\item{phasekmin}{Kmin parameter used when correcting phasing mistakes (Default 3)}
+\item{phasekmin}{Kmin parameter used when correcting phasing mistakes (Default: 3)}
+
+\item{calc_seg_baf_option}{Various options to recalculate the BAF of a segment. Options are: 1 - median, 2 - mean. (Default: 1)}
 }
 \description{
 This function performs segmentation. This is done in two steps. First a segmentation step

man/segment.baf.phased.sv.Rd

@@ -5,7 +5,8 @@
 \title{Segment BAF with the inclusion of structural variant breakpoints}
 \usage{
 segment.baf.phased.sv(samplename, inputfile, outputfile, svs, gamma = 10,
-  phasegamma = 3, kmin = 3, phasekmin = 3, no_segmentation = F)
+  phasegamma = 3, kmin = 3, phasekmin = 3, no_segmentation = F,
+  calc_seg_baf_option = 1)
 }
 \arguments{
 \item{samplename}{Name of the sample, which is used to name output figures}
@@ -25,6 +26,8 @@ segment.baf.phased.sv(samplename, inputfile, outputfile, svs, gamma = 10,
 \item{phasekmin}{Kmin parameter used when correcting phasing mistakes (Default 3)}
 
 \item{no_segmentation}{Do not perform segmentation. This step will switch the haplotype blocks, but then just takes the mean BAFphased as BAFsegm}
+
+\item{calc_seg_baf_option}{Various options to recalculate the BAF of a segment. Options are: 1 - median, 2 - mean. (Default: 1)}
 }
 \description{
 This function takes the SV breakpoints as initial segments and runs PCF on each