segmentationPSCBS {PureCN} | R Documentation |
Alternative segmentation function using the PSCBS
package. This
function is called via the fun.segmentation
argument of
runAbsoluteCN
. The arguments are passed via
args.segmentation
.
segmentationPSCBS(normal, tumor, log.ratio, seg, plot.cnv, sampleid, target.weight.file = NULL, 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, ...)
normal |
Coverage data for normal sample. |
tumor |
Coverage data for tumor sample. |
log.ratio |
Copy number log-ratios, one for each exon in coverage file. |
seg |
If segmentation was provided by the user, this data structure will contain this segmentation. Useful for minimal segmentation functions. Otherwise PureCN will re-segment the data. This segmentation function ignores this user provided segmentation. |
plot.cnv |
Segmentation plots. |
sampleid |
Sample id, used in output files. |
target.weight.file |
Can be used to assign weights to targets. NOT SUPPORTED YET in segmentation. Will remove targets with weight below 1/3. |
alpha |
Alpha value for CBS, see documentation for the |
undo.SD |
|
flavor |
Flavor value for PSCBS. See |
tauA |
tauA argument for PSCBS. See |
vcf |
Optional VCF object with germline allelic ratios. |
tumor.id.in.vcf |
Id of tumor in case multiple samples are stored in VCF. |
normal.id.in.vcf |
Id of normal in in VCF. If |
max.segments |
If not |
prune.hclust.h |
Height in the |
prune.hclust.method |
Cluster method used in the |
chr.hash |
Mapping of non-numerical chromsome names to numerical names
(e.g. chr1 to 1, chr2 to 2, etc.). If |
centromeres |
A |
... |
Additional parameters passed to the
|
data.frame
containing the segmentation.
Markus Riester
Olshen, A. B., Venkatraman, E. S., Lucito, R., Wigler, M. (2004). Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5: 557-572.
Venkatraman, E. S., Olshen, A. B. (2007). A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23: 657-63.
Olshen et al. (2011). Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. Bioinformatics.
normal.coverage.file <- system.file("extdata", "example_normal.txt", package="PureCN") tumor.coverage.file <- system.file("extdata", "example_tumor.txt", package="PureCN") vcf.file <- system.file("extdata", "example_vcf.vcf.gz", package="PureCN") interval.file <- system.file("extdata", "example_intervals.txt", package="PureCN") # The max.candidate.solutions, max.ploidy and test.purity parameters are set to # non-default values to speed-up this example. This is not a good idea for real # samples. ret <-runAbsoluteCN(normal.coverage.file=normal.coverage.file, tumor.coverage.file=tumor.coverage.file, vcf.file=vcf.file, genome="hg19", sampleid="Sample1", interval.file=interval.file, fun.segmentation=segmentationPSCBS, max.ploidy=4, test.purity=seq(0.3,0.7,by=0.05), max.candidate.solutions=1)