processMultipleSamples {PureCN} | R Documentation

## 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,
      interval.weight.file = 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.
`interval.weight.file` | Can be used to assign weights to intervals.
`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.

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

    interval.weight.file <- "interval_weights.txt"
    normal.coverage.files <- c(normal1.coverage.file, normal2.coverage.file)
    tumor.coverage.files <- c(tumor1.coverage.file, tumor2.coverage.file)

    calculateIntervalWeights(normal.coverage.files, interval.weight.file)
    normalDB <- createNormalDatabase(normal.coverage.files)

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

[Package PureCN version 1.14.3 Index]