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Jun 17, 2021
Sep 7, 2018
Jun 26, 2020

gassocplot

Regional association plots for genetic and epigenetic data. gassocplot2 is now available, which enables use of build 38 (hg38) coordinates in addition to GRCh37 (hg19) coordinates as well as incorporating additional marker labelling.

Functions

  • assoc_plot - plots a regional association plot or fine-mapping probability plot for a single trait within a genomic region based on GRCh37 (hg19) coordinates.
  • assoc_plot_save - saves a PNG of the assoc_plot.
  • stack_assoc_plot - plots a stacked regional association plot for multiple traits within a genomic region based on GRCh37 (hg19) coordinates.
  • stack_assoc_plot_save - saves a PNG of the stack_assoc_plot.

Installation

  1. install.packages("devtools")
  2. library(devtools)
  3. install_github("jrs95/gassocplot")
  4. library(gassocplot)

Examples

### assoc_plot
markers <- gassocplot::test_assoc_plot
head(markers)
corr <- gassocplot::test_corr # this is correlation not correlation squared and has to be ordered in the same way as the markers data frame
plot <- assoc_plot(markers, corr)
assoc_plot_save(plot, "assoc_plot_test.png")

### stack_assoc_plot
markers <- gassocplot::test_stack_assoc_plot_markers
head(markers)
z <- gassocplot::test_stack_assoc_plot_associations
head(z)
corr <- gassocplot::test_corr # this is correlation not correlation squared and has to be ordered in the same way as the markers data frame
plot <- stack_assoc_plot(markers, z, corr, traits=c("Trait 1", "Trait 2"))
stack_assoc_plot_save(plot, "stack_assoc_plot_test.png", 2)

Linkage disequilibrium information

The LDlinkR package can be used to obtain linkage disequilibrium matrices from 1000G using the LDmatrix function. Note the matrix from this function would have to be square rooted and ordered in the same way as the markers data frame.

Citation

Please cite this R package using the link: https://github.com/jrs95/gassocplot

Plots

Regional association plot

Stacked regional association plot

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Regional association plotter for genetic and epigenetic data

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