Posts Tagged ‘ GWAS ’

A New Dimension to Principal Components Analysis

October 27, 2011
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A New Dimension to Principal Components Analysis

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
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More Command-Line Text Munging Utilities

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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More Command-Line Text Munging Utilities

May 19, 2011
By
More Command-Line Text Munging Utilities

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...

Read more »

PLINK/SEQ for Analyzing Large-Scale Genome Sequencing Data

May 4, 2011
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PLINK/SEQ is an open source C/C++ library for analyzing large-scale genome sequencing data. The library can be accessed via the pseq command line tool, or through an R interface. The project is developed independently of PLINK but it's syntax will be f...

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PLINK/SEQ for Analyzing Large-Scale Genome Sequencing Data

May 4, 2011
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PLINK/SEQ for Analyzing Large-Scale Genome Sequencing Data

PLINK/SEQ is an open source C/C++ library for analyzing large-scale genome sequencing data. The library can be accessed via the pseq command line tool, or through an R interface. The project is developed independently of PLINK but it's syntax will be f...

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Annotated Manhattan plots and QQ plots for GWAS using R, Revisited

April 25, 2011
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Last year I showed you how to create manhattan plots, and later how to highlight regions of interest, using ggplot2 in R. The code was slow, required a lot of memory, and was difficult to maintain and modify.I finally found time to rewrite the code u...

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Annotated Manhattan plots and QQ plots for GWAS using R, Revisited

April 25, 2011
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Annotated Manhattan plots and QQ plots for GWAS using R, Revisited

Last year I showed you how to create manhattan plots, and later how to highlight regions of interest, using ggplot2 in R. The code was slow, required a lot of memory, and was difficult to maintain and modify.I finally found time to rewrite the code usi...

Read more »

Using R + Bioconductor to Get Flanking Sequence Given Genomic Coordinates

April 12, 2011
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I'm working on a project using next-gen sequencing to fine-map a genetic association in a gene region. Now that I've sequenced the region in a small sample, I'm picking SNPs to genotype in a larger sample. When designing the genotyping assay the lab wi...

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Using R + Bioconductor to Get Flanking Sequence Given Genomic Coordinates

April 12, 2011
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Using R + Bioconductor to Get Flanking Sequence Given Genomic Coordinates

I'm working on a project using next-gen sequencing to fine-map a genetic association in a gene region. Now that I've sequenced the region in a small sample, I'm picking SNPs to genotype in a larger sample. When designing the genotyping assay the lab wi...

Read more »

Prune GWAS data in R

March 29, 2011
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Prune GWAS data in R

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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