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.
Vignettes
-
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