baf_plot: baf_plot

In knausb/coveRage: Tools to Explore Sequencing Coverage in High-Throughput Sequencing Projects

Description

B allele frequency plot.

Usage

baf_plot(counts, alpha = 255, title = "Locus", na.rm = FALSE,
  aline = c(0, 0.25, 0.33, 0.5, 0.66, 0.75, 1), hline = c(0.25, 0.33, 0.5,
  0.66, 0.75), halpha = 255, vline = NULL, valpha = 255, ...)

Arguments

counts	a numeric matrix containing count data
alpha	opacity (0-255)
title	for the plot.
na.rm	Logical, should sites which contain NAs (no reported coverage) be removed
aline	coordinates at which to draw tick marks on the y axis
hline	coordinates at which to draw horizontal lines where NULL omits lines
halpha	opacity (0-255) for horizontal lines
vline	coordinates at which to draw vertical lines where NULL omits lines
valpha	opacity (0-255) for vertical lines
...	arguments to be passed to methods

Details

Plots coverage and allele frequencies for a chromosomal region. The upper pane presents per site sequencing depth while the lower pane presents the frequency of all four alleles. These plots can be used to identify technical error (i.e., read alignment issues) and/or biological phenomena such as copy number variation.

The matrix of count data can be generated from mpileup data with the function baf_stats

References

Laurie, Cathy C, Kimberly F Doheny, Daniel B Mirel, Elizabeth W Pugh, Laura J Bierut, Tushar Bhangale, Frederick Boehm, Neil E Caporaso, Marilyn C Cornelis, Howard J Edenberg and others. 2010. Quality control and quality assurance in genotypic data for genome-wide association studies. Genetic Epidemiology 34(6): 591–602.

See Also

baf_stats

knausb/coveRage documentation built on May 20, 2019, 12:52 p.m.