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.

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
https://github.com/psobczyk/geneSLOPE

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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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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