Learn R Programming


geneSLOPE -- Genome Wide Association Study with SLOPE

Package geneSLOPE can be used to perform Genome-wide association study with SLOPE.

Such an analysis is split into three steps.

  1. Data is read and immediately screened using a marginal test for each SNP.
  2. SNPs are clumped based on correlations.
  3. SLOPE is performed on reduced data. Each clump is represented by one SNP.

How do I get set up?

You can install the latest development version of the code using the devtools R package.

# Install devtools, if you haven't already.
install.packages("devtools")

library(devtools)
install_github("psobczyk/geneSLOPE")

  • You might need to install package dependencies:
    • SLOPE
    • ggplot2
    • bigmemory
    • grid
  • Read vignette "Tutorial for GWAS with SLOPE" to get familiar with basic usage

Running GUI

GUI based on shiny R package is available

library(geneSLOPE)
gui_geneSLOPE()

Who do I talk to?

  • If help provided in the package documentation does not solve your problem

please contact Piotr.Sobczyk[at]pwr.edu.pl


Research reported in this software was supported by National Institutes of Health under award number R01 HG006695.


This project has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no 602552.

Copy Link

Version

Install

install.packages('geneSLOPE')

Monthly Downloads

181

Version

0.38.2

License

GPL-3

Issues

Pull Requests

Stars

Forks

Maintainer

Last Published

August 16th, 2023

Functions in geneSLOPE (0.38.2)

create_lambda

Lambda sequences for SLOPE
clump_snps

Clumping procedure for SLOPE
identify_clump.selectionResult

Identify clump number in selectionResult class plot
identify_clump.clumpingResult

Identify clump number in clumpingResult class plot
print.selectionResult

Print selectionResult class object
screeningResult

screeningResult class
read_phenotype

Read phenotype from .fam file
screen_snps

Reading and screening SNPs from .raw file and
gui_geneSLOPE

GUI for GWAS with SLOPE
plot.clumpingResult

Plot clumpingResult class object
identify_clump

identify_clump
phenotypeData

phenotypeData class
print.phenotypeData

Print phenotypeData class object
print.screeningResult

Print function for class screeningResult class
summary.phenotypeData

Summary phenotypeData class object
summary.clumpingResult

Summary clumpingResult class object
plot.selectionResult

Plot selectionResult class object
summary.screeningResult

Summary function for class screeningResult
summary.selectionResult

Summary selectionResult class object
select_snps

GWAS with SLOPE
print.clumpingResult

Print clumpingResult class object
selectionResult

selectionResult class
geneSLOPE

Genome-Wide Association Study with SLOPE
clumpingResult

clumpingResult class