plot_snp_module: Ideogram of a SNP module.

In hclimente/blur: Visualization utilities after using martini

Description

Create a ideogram of a SNP module from SConES results using the Gviz package (Hahne and Ivanek, 2016).

Usage

plot_snp_module(cones, k, genome = "hg19")

Arguments

cones	Results from SConES.
k	Id of the module to plot.
genome	Abbreviations of the genome to use: hg19 for human (default), mm10 for mouse, etc. Argument to be passed to IdeogramTrack.

Value

An ideogram per chromosome showing the selected SNPs and the genes in the region.

References

Hahne F. and Ivanek R. (2016). "Statistical Genomics: Methods and Protocols." In Mathe E and Davis S (eds.), chapter Visualizing Genomic Data Using Gviz and Bioconductor, pp. 335-351. Springer New York, New York, NY. ISBN 978-1-4939-3578-9, doi: 10.1007/978-1-4939-3578-9_16, http://dx.doi.org/10.1007/978-1-4939-3578-9_16.

hclimente/blur documentation built on Nov. 28, 2020, 11:12 a.m.