snpStats: Overview

This package extends the snpMatrix package, allowing uncertainty in genotype assignments, for example as consequence of imputation. It provides most of the functionality of snpMatrix, although a few functions differ somewhat from their predecessors. It also provides several new functions. Classes have had to be renamed but are mostly compatible with those in snpMatrix, and functions are included to convert these to their snpStats equivalents. However, the imputation rules objects in snpMatrix are not compatible with those now used and must be regenerated. For more details, see the "differences" vignette. Further development of the snpMatrix project by this developer will take place entirely within snpStats.


Differences between the snpMatrix and snpStats packages:
Equivalent classes and differences in behaviour
Example of genome-wide association testing:
Introduction to snpStats for analysis of GWA studies
Data input in snpStats:
Reading genotype data from various input file formats
Imputation and meta-analysis:
Imputed SNP analyses and meta-analysis with snpStats
LD vignette:
Measures of linkage disequilibrium
PCA vignette:
Principal components analysis with snpStats
TDT vignette:
Use of snpStats in family--based association studies