adams-charleen / mrgwasss

MrGWASSS Cleans and Visualizes GWAS Summary Statistics

MrGWASSS

MrGWASSS cleans and visualizes GWAS summary statistics

Dependencies

Depends: 
    BioThingsClient.R (>= 0.99.1),
    devtools,
    dplyr,
    ggplot2,
    ggpubr,
    knitr,
    latex2exp,
    purrr,
    writexl
Remotes:  
    biothings/BioThingsClient.R

Usage

Load the package

# Load the package
if(!require("MrGWASSS")){
  devtools::install_github("Broccolito/MrGWASSS")
  library(MrGWASSS)
}

Load GWAS summary statistics into the workspace

Given the load_data function arguments:

load_data(
  file_name = "FHS_EA_MRS_5e8_snplist.txt",
  marker_name_column = "SNPID",
  chr_column = "CHR",
  pos_column = "POS",
  ref_column = "NEA",
  alt_column = "EA",
  pvalue_column = "p.value",
  delimiter = " "
)

To load the summary statistics from SAIGE, use:

data = load_data("HAPO_AA_Ogtt_diff_chr_MERGED.txt", 
                 by_marker = TRUE, 
                 marker_name_column = "SNPID", 
                 pvalue_column = "p.value", 
                 delimiter = " ")

To load the summary statistics from METAL, use:

data = load_data("METAANALYSIS1.TBL",
                 by_marker = TRUE,
                 marker_name_column = "MarkerName",
                 pvalue_column = "P.value",
                 delimiter = "\t")

Threshold the summary statistics

data_1e5 = threshold_data(data, 1e-5)

Annotate the stats

data_annotated = annotate_data(data_1e5)

Make Manhattan plots

plot_manhattan(data)

Make Q-Q plot

plot_qq(data)