Tools to Create Gene Sets

A set of functions to create SQL tables of gene and SNP information and compose them into a SNP Set, for example for use with the RSNPset package, or to export to a PLINK set.


snplist v0.18.1 (Release date: 2017-12-11)

  • Bug fix for drop table error. Now makeGeneSet() always makes annoTable as TABLE (never as VIEW)

snplist v0.18 (Release date: 2017-08-14)

  • Now requires RSQLite >=1.1 (changed calls of dbGetQuery to dbExecute)
  • Added calls to: ‘R_registerRoutines’ and ‘R_useDynamicSymbols’
  • Bug fix to prevent Latex error when using TeXLive 2017

snplist v0.17 (Release date: 2016-12-13)

  • setSNPTable() and setGeneTable now force 'chr' to be character and 'pos', 'start', and 'end' to be numeric before populating the SQL tables to ensure values are comparable between the two.

snplist v0.16 (Release date: 2016-10-27)

  • makeGeneSet() updated to correct warning when deleting existing SQL views
  • Vignette updated to access GRCh37 SNP positions from Ensembl

snplist v0.15 (Release date: 2015-11-05)

  • getBioMartData() updated to allow users to specify the Ensembl data mart

snplist v0.14 (Release date: 2015-09-18)

  • Addition of NEWS file
  • Bug fix to prevent warnings of multiple comparisons in setSNPTable() and makeGeneSet() functions when first argument is a data.frame instead of a file name
  • Missing required column names in setSNPTable() and makeGeneSet() functions now results in stop() instead of return(print())

snplist v0.13 (Release date: 2014-12-03)

  • Change of Maintainer
  • Added DBI to Imports in DOCUMENTATION and in NAMESPACE

Reference manual

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0.18.1 by Alexander Sibley, a year ago

Browse source code at

Authors: Chanhee Yi , Alexander Sibley , and Kouros Owzar

Documentation:   PDF Manual  

GPL-3 license

Imports biomaRt, Rcpp, R.utils, DBI

Depends on RSQLite

Suggests knitr

Linking to Rcpp

Imported by MetaIntegrator.

Suggested by groupedSurv.

See at CRAN