preprocessIntervals: Preprocess intervals

Description Usage Arguments Value Author(s) References Examples

View source: R/preprocessIntervals.R

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

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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(0.5, 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

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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")

PureCN documentation built on Nov. 8, 2020, 5:37 p.m.