tallyPlot {Rariant} | R Documentation |
Create a mismatch plot from a list of BAM files directly.
tallyPlot(file, region, ref, nCycles = 0, minQual = 0, minFreq = 0, ...)
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'. |
A 'ggplot2' or 'ggbio' object.
h5vc::mismatchPlot
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)