Version 1.1 Changelog:

Major:
A vignette (postgwasVignette) has been added.
GenABEL, GEMMA and FAsT-LMM output can be read by default. 
buffer data concept changed (see help(postgwasBuffer)).  
gwas2network: The legend of graphs can now be plotted to a separate box (new default)
gwas2network: Major change in community p-value calculations and GO enrichment (see documentation)
gwas2network: topGO enrichment tree can now be plotted (depending on file.verbosity argument)
gwas2network: singleton, unconnected vertices now remain part of the network
gwas2network: Improved runtime and memory consumption (e.g. uses data.tables) 
Manhattanplot: Bug on sorting chromosomes with mixed character / numerical values fixed
Manhattanplot: Bug for identifying highlighted regions with multiple thresholds fixed
Manhattanplot: Gene annotation now draws SNP identifier when no genes can be annotated
Manhattanplot: Can draw calibration lines now (argument highlight.lines)
getGenotypes: Extended, now also handles GenABEL (gwaa) files
getGenotypes: Extended, can now write retrieved genotypes to ped/map and gwaa/phe files
getGenotypes: Default argument list and return value definition has been changed 
Snp2gene: Argument list changed
RemoveNeighborSnps: Bugfix in p-value pruning version for certain overlapping region constellations
getInteractions: getInteractions.ppi has been removed due to unavailability of the REST access to biogrid. 
                 A new getInteractions.path function has been added to generate networks of pathway data from REACTOME biomart. 

Minor:
Manhattanplot: Proportions and scaling of graphical elements optimized
Snp2gene: Bugfix for reporting table
biomartAccess: downloaded GO terms can now be buffered