filterIntervals {PureCN} | R Documentation

## Remove low quality intervals

### Description

This function determines which intervals in the coverage files should be included or excluded in the segmentation. It is called via the `fun.filterIntervals` argument of `runAbsoluteCN`. The arguments are passed via `args.filterIntervals`.

### Usage

    filterIntervals(
      normal,
      tumor,
      log.ratio,
      seg.file,
      filter.lowhigh.gc = 0.001,
      min.coverage = 15,
      min.total.counts = 100,
      min.targeted.base = 5,
      min.mappability = c(0.6, 0.1),
      min.fraction.offtarget = 0.05,
      normalDB = NULL
    )

### Arguments

`normal` | Coverage data for normal sample.
`tumor` | Coverage data for tumor sample.
`log.ratio` | Copy number log-ratios, one for each interval in the coverage file.
`seg.file` | If not `NULL`, then do not filter intervals, because data is already segmented via the provided segmentation file.
`filter.lowhigh.gc` | Quantile q (defines lower q and upper 1-q) for removing intervals with outlier GC profile. Assuming that GC correction might not have been worked on those. Requires `interval.file`.
`min.coverage` | Minimum coverage in both normal and tumor. Intervals with lower coverage are ignored. If a `normalDB` is provided, then this database already provides information about low quality intervals and the `min.coverage` is set to `min.coverage/10000`.
`min.total.counts` | Exclude intervals with fewer than that many reads in combined tumor and normal.
`min.targeted.base` | Exclude intervals with targeted base (size in bp) smaller than this cutoff. This is useful when the same interval file was used to calculate GC content. For such small targets, the GC content is likely very different from the true GC content of the probes.
`min.mappability` | `double(2)` specifying the minimum mappability score for on-target, off-target in that order.
`min.fraction.offtarget` | Skip off-target regions when less than the specified fraction of all intervals passes all filters
`normalDB` | Normal database, created with `createNormalDatabase`.

### Value

`logical(length(log.ratio))` specifying which intervals should be used in segmentation.

### Author(s)

Markus Riester

### Examples

    normal.coverage.file <- system.file("extdata", "example_normal.txt",
        package = "PureCN")
    normal2.coverage.file <- system.file("extdata", "example_normal2.txt",
        package = "PureCN")
    normal.coverage.files <- c(normal.coverage.file, normal2.coverage.file)
    normalDB <- createNormalDatabase(normal.coverage.files)

    tumor.coverage.file <- system.file("extdata", "example_tumor.txt",
        package = "PureCN")
    vcf.file <- system.file("extdata", "example.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,
        genome = "hg19", vcf.file = vcf.file, normalDB = normalDB,
        sampleid = "Sample1", interval.file = interval.file,
        args.filterIntervals = list(min.targeted.base = 10), max.ploidy = 4,
        test.purity = seq(0.3, 0.7, by = 0.05), max.candidate.solutions = 1)

[Package PureCN version 2.0.2 Index]