plotAlignmentIdentity: plot a histogram of mapping identities

Description Usage Arguments Value Examples

View source: R/AlignmentPlots.R

Description

This method will plot a histogram of mapping identities

Usage

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plotAlignmentIdentity(bamFile, flag = 'Primary', lower = 0.7,
    upper = 1, segments = 50)

Arguments

bamFile

is the path to the bamFile to plot

flag

is the flagged sequence type to plot [Primary]

lower

lower limit for plotting values

upper

upper limit for plotting values

segments

number of segments to split data into

Value

a ggplot2 object

Examples

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demoBam <- system.file("extdata",
    "cas9_FAK76554.bam",
    package = "nanopoRe")
bamSummary <- bamSummarise(demoBam, blockSize=1000L)
plotAlignmentIdentity()

sagrudd/nanopoRe documentation built on June 7, 2020, 10:20 p.m.