R packages

coloc

CRAN github Note the github repository has important bug fixes that haven’t reached CRAN.

a package of R functions used to test for colocalisation of two genetic traits. For more detail or the statistical background and applications see:

colocCommonControl

CRAN // github Adaptation of coloc for comparing two GWAS studies which share controls

snpStatsWriter

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.

wgsea

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

extraBinomial

CRAN

(author Xin Yang, listed here because Xin doesn’t have her own website) uses an extra binomial model to test for case-control allele frequency differences in pooled sequence data. See Yang X, Todd JA, Clayton D, and Wallace C. Extra-binomial variation approach for analysis of pooled DNA sequencing data. /Bioinformatics/ 2012. [ Europe PMC ]

R packages from github

To install these from github, do, in R: #+BEGIN_SRC R install.packages(“devtools”) library(devtools) install_github(“chr1swallace/package.name”, “chr1swallace”) #+END_SRC

annotSnpStats

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.

GUESSFM

github A wrapper around the GUESS stochastic model search method for fine mapping causal variants in genetic data. See more detail here.

origin

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 ]

Non-R packages

VSEAMS (Olly Burren)

Variant set enrichment analysis (of association summary statistics) using multivariate sampling. Please see the wiki available at this wiki for further details. Method described in }

See also…

published R packages on CRAN // all code at github // code blog