tallyPlot {Rariant} | R Documentation

## Mismatch plot from BAM files

### 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)

[Package Rariant version 1.16.0 Index]