processMultipleSamples: Multi sample normalization and segmentation

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

Multi sample normalization and segmentation

Description

This function performs normalization and segmentation when multiple for the same patient are available.

Usage

processMultipleSamples(
  tumor.coverage.files,
  sampleids,
  normalDB,
  num.eigen = 20,
  genome,
  plot.cnv = TRUE,
  w = NULL,
  min.interval.weight = 1/3,
  max.segments = NULL,
  chr.hash = NULL,
  centromeres = NULL,
  ...
)

Arguments

tumor.coverage.files	Coverage data for tumor samples.
sampleids	Sample ids, used in output files.
normalDB	Database of normal samples, created with createNormalDatabase.
num.eigen	Number of eigen vectors used.
genome	Genome version, for example hg19. Needed to get centromere positions.
plot.cnv	Segmentation plots.
w	Weight of samples. Can be used to downweight poor quality samples. If NULL, sets to inverse of median on-target duplication rate if available, otherwise does not do any weighting.
min.interval.weight	Can be used to ignore intervals with low weights.
max.segments	If not NULL, try a higher undo.SD parameter if number of segments exceeds the threshold.
chr.hash	Mapping of non-numerical chromsome names to numerical names (e.g. chr1 to 1, chr2 to 2, etc.). If NULL, assume chromsomes are properly ordered.
centromeres	A GRanges object with centromere positions.
...	Arguments passed to the segmentation function.

Details

CURRENTLY DEFUNCT BECAUSE IT DEPENDS ON THE DEFUNCT COPYNUMBER PACKAGE. We are working on a replacement.

Value

data.frame containing the segmentation.

Author(s)

Markus Riester

References

Nilsen G., Liestol K., Van Loo P., Vollan H., Eide M., Rueda O., Chin S., Russell R., Baumbusch L., Caldas C., Borresen-Dale A., Lingjaerde O. (2012). "Copynumber: Efficient algorithms for single- and multi-track copy number segmentation." BMC Genomics, 13(1), 591.

See Also

runAbsoluteCN

Examples

normal1.coverage.file <- system.file("extdata", "example_normal.txt.gz",
    package = "PureCN")
normal2.coverage.file <- system.file("extdata", "example_normal2.txt.gz",
    package = "PureCN")
tumor1.coverage.file <- system.file("extdata", "example_tumor.txt.gz",
    package = "PureCN")
tumor2.coverage.file <- system.file("extdata", "example_tumor2.txt.gz",
    package = "PureCN")

normal.coverage.files <- c(normal1.coverage.file, normal2.coverage.file)
tumor.coverage.files <- c(tumor1.coverage.file, tumor2.coverage.file)

normalDB <- createNormalDatabase(normal.coverage.files)

# seg <- processMultipleSamples(tumor.coverage.files,
#         sampleids = c("Sample1", "Sample2"),
#         normalDB = normalDB,
#         genome = "hg19")

lima1/PureCN documentation built on Sept. 17, 2024, 5:48 a.m.