geneSLOPE: Genome-Wide Association Study with SLOPE
Version 0.37.0

Genome-wide association study (GWAS) performed with SLOPE, short for Sorted L-One Penalized Estimation, a method for estimating the vector of coefficients in linear model. In the first step of GWAS, SNPs are clumped according to their correlations and distances. Then, SLOPE is performed on data where each clump has one representative.

AuthorDamian Brzyski [aut], Christine Peterson [aut], Emmanuel J. Candes [aut], Malgorzata Bogdan [aut], Chiara Sabatti [aut], Piotr Sobczyk [cre, aut]
Date of publication2016-10-26 15:43:08
MaintainerPiotr Sobczyk <piotr.sobczyk@pwr.edu.pl>
LicenseGPL-3
Version0.37.0
URL https://github.com/psobczyk/geneSLOPE
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("geneSLOPE")

Getting started

Tutorial for GWAS with SLOPE

Popular man pages

geneSLOPE: Genome-Wide Association Study with SLOPE
gui_geneSLOPE: GUI for GWAS with SLOPE
identify_clump: identify_clump
identify_clump.selectionResult: Identify clump number in selectionResult class plot
phenotypeData: phenotypeData class
plot.clumpingResult: Plot clumpingResult class object
read_phenotype: Read phenotype from .fam file
See all...

All man pages Function index File listing

Man pages

clumpingResult: clumpingResult class
clump_snps: Clumping procedure for SLOPE
geneSLOPE: Genome-Wide Association Study with SLOPE
gui_geneSLOPE: GUI for GWAS with SLOPE
identify_clump: identify_clump
identify_clump.clumpingResult: Identify clump number in clumpingResult class plot
identify_clump.selectionResult: Identify clump number in selectionResult class plot
phenotypeData: phenotypeData class
plot.clumpingResult: Plot clumpingResult class object
plot.selectionResult: Plot selectionResult class object
print.clumpingResult: Print clumpingResult class object
print.phenotypeData: Print phenotypeData class object
print.screeningResult: Print function for class screeningResult class
print.selectionResult: Print selectionResult class object
read_phenotype: Read phenotype from .fam file
screeningResult: screeningResult class
screen_snps: Reading and screening SNPs from .raw file and
selectionResult: selectionResult class
select_snps: GWAS with SLOPE
summary.clumpingResult: Summary clumpingResult class object
summary.phenotypeData: Summary phenotypeData class object
summary.screeningResult: Summary function for class screeningResult
summary.selectionResult: Summary selectionResult class object

Functions

clump_snps Man page Source code
clumpingResult Man page
clumpingResult_no_info_print Source code
create_clumping_plot_data Source code
create_slope_plot_data Source code
estimate_noise Source code
geneSLOPE Man page
geneSLOPE-package Man page
gui_geneSLOPE Man page Source code
identify_clump Man page Source code
identify_clump.clumpingResult Man page Source code
identify_clump.selectionResult Man page Source code
pValComp Source code
phenotypeData Man page
plot.clumpingResult Man page Source code
plot.selectionResult Man page Source code
print.clumpingResult Man page Source code
print.phenotypeData Man page Source code
print.screeningResult Man page Source code
print.selectionResult Man page Source code
read_phenotype Man page Source code
replace_na_with_mean Source code
screen_snps Man page Source code
screeningResult Man page
select_snps Man page Source code
selectionResult Man page
summary.clumpingResult Man page Source code
summary.phenotypeData Man page Source code
summary.screeningResult Man page Source code
summary.selectionResult Man page Source code

Files

inst
inst/shiny-examples
inst/shiny-examples/genSLOPE_gui
inst/shiny-examples/genSLOPE_gui/ui.R
inst/shiny-examples/genSLOPE_gui/server.R
inst/extdata
inst/extdata/plinkPhenotypeExample.fam
inst/extdata/plinkDataExample.raw
inst/extdata/plinkMapExample.map
inst/doc
inst/doc/GWASwithSLOPE.Rmd
inst/doc/GWASwithSLOPE.R
inst/doc/GWASwithSLOPE.html
tests
tests/testthat.R
tests/testthat
tests/testthat/test_screen_snps.R
NAMESPACE
R
R/screen_snps.R
R/identify_clump.R
R/auxilliary.R
R/select_snps.R
R/gui_geneSLOPE.R
R/selectionResult.R
R/read_phenotype.R
R/clump_snps.R
R/geneSLOPE.R
R/clumpingResult.R
R/phenotypeData.R
R/screeningResult.R
vignettes
vignettes/GWASwithSLOPE.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/print.screeningResult.Rd
man/summary.screeningResult.Rd
man/select_snps.Rd
man/clump_snps.Rd
man/screen_snps.Rd
man/plot.selectionResult.Rd
man/print.selectionResult.Rd
man/plot.clumpingResult.Rd
man/print.phenotypeData.Rd
man/gui_geneSLOPE.Rd
man/read_phenotype.Rd
man/phenotypeData.Rd
man/screeningResult.Rd
man/identify_clump.clumpingResult.Rd
man/summary.phenotypeData.Rd
man/summary.clumpingResult.Rd
man/selectionResult.Rd
man/identify_clump.selectionResult.Rd
man/print.clumpingResult.Rd
man/summary.selectionResult.Rd
man/geneSLOPE.Rd
man/identify_clump.Rd
man/clumpingResult.Rd
geneSLOPE documentation built on May 19, 2017, 11:33 p.m.

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