To install R packages directly from github, do, in R:
install.packages("devtools") library(devtools) install_github("chr1swallace/package.name")
New in v3.1 which is now up to date on CRAN:
finemap.abf() offers finemapping of single traits under a single causal variant assumption. See vignette for details.
github // extends SnpMatrix objects from the snpStats package by tying in sample and snp annotation data.frames. It allows the joint manipulation, and binding, of such objects, and includes a few functions I use for finding duplicate samples, applying QC, and aligning alleles between different datasets. It seems to work, and I intend to push it to CRAN in the future.
github // allows writing snpStats objects to disk in formats suitable for reading by snphap, phase, mach, IMPUTE, beagle, and (almost) anything else that expects a rectangular format.
CRAN // implements a Wilcoxon-based test for Gene Set Enrichment Analysis when testing regions of the genome according to GWAS derived evidence for SNP-trait association. For more detail, see the supplementary methods of (5).
github // implements an extension to the Weinberg method for testing for parent of origin effects to allow for multiple affected offspring in a nuclear family. I haven’t used it in a while, and it requires some checking just to get it to pass the CRAN tests. Unless I need to revisit it for another reason, I am unlikely to push it to CRAN, but it is a finished package. For more detail see:
Weinberg et al. Methods for detection of parent-of-origin effects in genetic studies of case-parents triads. /Am J Hum Genet/ 65:229-235. 1999.
Wallace et al. The imprinted DLK1-MEG3 gene region on chromosome 14q32.2 alters susceptibility to type 1 diabetes. /Nat Genet/ 2010. [ Europe PMC ]