A New Dimension to Principal Components Analysis

October 27, 2011 | 0 Comments

In general, the standard practice for correcting for population stratification in genetic studies is to use principal components analysis (PCA) to categorize samples along different ethnic axes.  Price et al. published on this in 20...
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More Command-Line Text Munging Utilities

May 19, 2011 | 0 Comments

In a previous post I linked to gcol as a quick and intuitive alternative to awk. I just stumbled across yet another set of handy text file manipulation utilities from the creators of the BEAGLE software for GWAS data imputation and analysis. In additio...
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Prune GWAS data in R

March 29, 2011 | 0 Comments

Hansong Wang, our biostats professor here at the Hawaii Cancer Center, generously gave me some R code that goes through a SNP annotation file (i.e. a mapfile) and selects SNPs that are at least a certain specified distance apart. You might want to do t...
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New GenABEL Website, and more *ABEL software

March 18, 2011 | 0 Comments

The *ABEL suite of R packages and software for genetic analysis has grown substantially since the appearance of GenABEL and the previously mentioned ProbABEL R packages. There are now a handful of useful R packages and other software utilities facilita... [Read more...]

Efficient Mixed-Model Association in GWAS using R

April 13, 2010 | 0 Comments

I recently did an analysis for the eMERGE network where I had lots of individuals from a small town in central Wisconsin where many of the subjects were related to one another. The subjects could not be treated as independent, but I could not use a fam... [Read more...]

ProbABEL – R package for GWAS data imputation

April 6, 2010 | 0 Comments

I've been using GenABEL for some time now for GWAS analysis using related individuals. It has an excellent set of functions for estimating a kinship matrix from a dense marker panel and then using this in a linear mixed effects model to allow for relat... [Read more...]

Create annotated GWAS manhattan plots using ggplot2 in R

March 18, 2010 | 0 Comments

A few months ago I showed you in this post how to use some code I wrote to produce manhattan plots in R using ggplot2. The qqman() function I described in the previous post actually calls another function, manhattan(), which has a few options you can s... [Read more...]

LocusZoom: Plot regional association results from GWAS

February 10, 2010 | 0 Comments

Update Friday, May 14, 2010: See this newer post on LocusZoom. If you caught Cristen Willer's seminar here a few weeks ago you saw several beautiful figures in the style of a manhattan plot, but zoomed in around a region of interest, with several ot... [Read more...]

GWAS Manhattan plots and QQ plots using ggplot2 in R

January 20, 2010 | 0 Comments

Will posted earlier this week about how to produce manhattan plots of GWAS results using Stata, so I thought I'd share how I do this in R using ggplot2. First, if you've never used ggplot2, you'll need to add it to your R installation by typing: install.packages("ggplot2") Once ... [Read more...]

QQ plots of p-values in R using ggplot2

November 9, 2009 | 0 Comments

Way back will wrote on this topic.  See his previous post for Stata code for doing this.  Unfortunately the R package that was used to create QQ-plots here has been removed from CRAN, so I wrote my own using ggplot2 and some code I received from Daniel Shriner at NHGRI. ... [Read more...]

Visualizing sample relatedness in a GWAS using PLINK and R

October 9, 2009 | 0 Comments

Strict quality control procedures are extremely important for any genome-wide association study.  One of the first steps you should take when running QC on your GWAS is to look for related samples in your dataset.  This does two things for you.  First, you can get an idea of how many ... [Read more...]

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