preprocessIntervals {PureCN} | R Documentation

## Preprocess intervals

### Description

Optimize intervals for copy number calling by tiling long intervals and by including off-target regions. Uses `scanFa` from the Rsamtools package to retrieve GC content of intervals in a reference FASTA file. If provided, will annotate intervals with mappability and replication timing scores.

### Usage

    preprocessIntervals(
      interval.file,
      reference.file,
      output.file = NULL,
      off.target = FALSE,
      average.target.width = 400,
      min.target.width = 100,
      min.off.target.width = 20000,
      average.off.target.width = 2e+05,
      off.target.padding = -500,
      mappability = NULL,
      min.mappability = c(0.6, 0.1, 0.7),
      reptiming = NULL,
      average.reptiming.width = 1e+05,
      exclude = NULL,
      off.target.seqlevels = c("targeted", "all"),
      small.targets = c("resize", "drop")
    )

### Arguments

`interval.file` | File specifying the intervals. Interval is expected in first column in format CHR:START-END. Instead of a file, a `GRanges` object can be provided. This allows the use of BED files for example. Note that GATK interval files are 1-based (first position of the genome is 1). Other formats like BED files are often 0-based. The `import` function will automatically convert to 1-based `GRanges`.
`reference.file` | Reference FASTA file.
`output.file` | Optionally, write GC content file.
`off.target` | Include off-target regions.
`average.target.width` | Split large targets to approximately this size.
`min.target.width` | Make sure that target regions are of at least this specified width. See `small.targets`.
`min.off.target.width` | Only include off-target regions of that size
`average.off.target.width` | Split off-target regions to that
`off.target.padding` | Pad off-target regions.
`mappability` | Annotate intervals with mappability score. Assumed on a scale from 0 to 1, with score being 1/(number alignments). Expected as `GRanges` object with first meta column being the score. Regions outside these ranges are ignored, assuming that `mappability` covers the whole accessible genome.
`min.mappability` | `double(3)` specifying the minimum mappability score for on-target, off-target, and chrY regions in that order. The chrY regions are only used for sex determination in ‘PureCN’ and are therefore treated differently. Requires `mappability`.
`reptiming` | Annotate intervals with replication timing score. Expected as `GRanges` object with first meta column being the score.
`average.reptiming.width` | Tile `reptiming` into bins of specified width.
`exclude` | Any target that overlaps with this `GRanges` object will be excluded.
`off.target.seqlevels` | Controls how to deal with chromosomes/contigs found in the `reference.file` but not in the `interval.file`.
`small.targets` | Strategy to deal with targets smaller than `min.target.width`.

### Value

Returns GC content by interval as `GRanges` object.

### Author(s)

Markus Riester

### References

Talevich et al. (2016). CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing. PLoS Comput Biol.

### Examples

    reference.file <- system.file("extdata", "ex2_reference.fa",
        package = "PureCN", mustWork = TRUE)
    interval.file <- system.file("extdata", "ex2_intervals.txt",
        package = "PureCN", mustWork = TRUE)
    bed.file <- system.file("extdata", "ex2_intervals.bed",
        package = "PureCN", mustWork = TRUE)
    preprocessIntervals(interval.file, reference.file,
        output.file = "gc_file.txt")

    intervals <- import(bed.file)
    preprocessIntervals(intervals, reference.file,
        output.file = "gc_file.txt")

[Package PureCN version 2.0.2 Index]