From e9cdc68485ace98ca1765e0ce63ff6bc1c32bd8b Mon Sep 17 00:00:00 2001 From: James Staley Date: Wed, 17 May 2023 16:39:04 +0100 Subject: [PATCH] Update README.md (#4) --- README.md | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 41ae781..722287f 100644 --- a/README.md +++ b/README.md @@ -8,20 +8,23 @@ Regional association plots for genetic and epigenetic data. gassocplot2 is now [ * 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) +``` +install.packages("devtools") +library(devtools) +install_github("jrs95/gassocplot") +library(gassocplot) +``` ## Examples -\#\#\# assoc_plot +``` +### 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 +### stack_assoc_plot markers <- gassocplot::test_stack_assoc_plot_markers head(markers) z <- gassocplot::test_stack_assoc_plot_associations @@ -29,6 +32,7 @@ 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](https://cran.r-project.org/web/packages/LDlinkR/index.html) 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.