ReadPosErrorPlot: Plot distribution of errors by read position.
In ReQON: Recalibrating Quality Of Nucleotides

Description Usage Arguments Details Author(s) Examples

View source: R/ReadPosErrorPlot.R

Plots the number of sequencing errors by read position.

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ReadPosErrorPlot(ReadPosErrors, startpos = 1, error_col = "blue", thresh = 1.5, 
   thresh_col = "cyan", xlabel = "Read Position", ylabel = "# Errors", 
   main_title = "Distribution of Errors by Read Position")

`ReadPosErrors`	vector of sequencing error counts by read position.
`startpos`	Starting read position, typically 0 or 1. Default = 1.
`error_col`	color of line plotting the errors counts. Default = "blue".
`thresh`	Threshold for identifying read positions with large numbers of errors, plotted as a horizontal dashed line. Threshold is set as “thresh * (average number of errors per read position)”. Default = 1.5.
`thresh_col`	color of threshold line. Default = "cyan".
`xlabel`	x-axis label. Default = "Read Position".
`ylabel`	y-axis label. Default = "# Errors".
`main_title`	title. Default = "Distribution of Errors by Read Position".

ReadPosErrorPlot plots the distribution of sequencing errors by read position. If the input vector is $ReadPosErrors from ReQON output, this function will create the top left diagnostic plot that is output from ReQON.

For more details and interpretation, see the vignette by: browseVignettes("ReQON").

Christopher Cabanski ccabansk@genome.wustl.edu

## Create data of error counts 
x <- c( 1:30 )
err <- x^2 + ( 30 - x )^1.6 + rnorm(30, 0, 100)

## plot errors by read position
ReadPosErrorPlot( err )