mismatch-plot: Mismatch plot from BAM files

In julian-gehring/Rariant: Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies

Description

Create a mismatch plot from a list of BAM files directly.

Usage

  tallyPlot(file, region, ref, nCycles = 0, minQual = 0, minFreq = 0, ...)

Arguments

file	BAM file paths
region	GRanges with the position (width: 1) to tally, with one entry.
ref	Reference object, as 'BSgenome'.
nCycles	Number of sequencing cycles to remove from the beginning and end of each read when creating the base count table. This avoids low quality read positions [default: 0]. See 'tallyBamRegion'
minQual	Minimum base call quality for reads to be considered for the nucleotide count table [default: 0]. Reads with a lower quality are dropped. See 'tallyBamRegion'
minFreq	Currently not used
...	Additional arguments, passed to 'tallyBAM'.

Value

A 'ggplot2' or 'ggbio' object.

See Also

h5vc::mismatchPlot

Examples

  library(ggbio)
  library(GenomicRanges)
  library(BSgenome.Hsapiens.UCSC.hg19)

  region = GRanges("chr17", IRanges(7572100, width = 1))

  control_bam = system.file("extdata", "platinum", "control.bam", package =
  "Rariant", mustWork = TRUE)
  mix_bam = system.file("extdata", "platinum", "mix.bam", package = "Rariant",
  mustWork = TRUE)

  bam_files = c(control_bam, mix_bam)

  region = GRanges("chr17", IRanges(7572050, width = 100))

  control_bam = system.file("extdata", "platinum", "control.bam", package =
    "Rariant", mustWork = TRUE)
  test1_bam = system.file("extdata", "platinum", "test.bam", package =
    "Rariant", mustWork = TRUE)
  test2_bam = system.file("extdata", "platinum", "test2.bam", package =
    "Rariant", mustWork = TRUE)
  mix_bam = system.file("extdata", "platinum", "mix.bam", package =
    "Rariant", mustWork = TRUE)

  bam_files = c(control_bam, test1_bam, test2_bam, mix_bam)

  library(BSgenome.Hsapiens.UCSC.hg19)
  ref = BSgenome.Hsapiens.UCSC.hg19

  p = tracks(lapply(bam_files, tallyPlot, region, ref, minQual = 25))

  print(p)

julian-gehring/Rariant documentation built on May 20, 2019, 4:20 a.m.