geneSLOPE: Genome-Wide Association Study with SLOPE

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.

Author
Damian Brzyski [aut], Christine Peterson [aut], Emmanuel J. Candes [aut], Malgorzata Bogdan [aut], Chiara Sabatti [aut], Piotr Sobczyk [cre, aut]
Date of publication
2016-10-26 15:43:08
Maintainer
Piotr Sobczyk <piotr.sobczyk@pwr.edu.pl>
License
GPL-3
Version
0.37.0
URLs

View on CRAN

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

Files in this package

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