CHANGES IN VERSION 4.7 ---------------------- o The snplocsDefault() function has been added to simplify appropriate selection of SNPlocs.Hsapiens.dbSNP.* to a common value for all usages o The sensanal() function now operates on a sensiCisInput instance to help provide an overview of sensitivity analysis for cis-eQTL searches CHANGES IN VERSION 4.6 ---------------------- o The primary tools for one-population analyses are best.cis.eQTLs and transScores. Multipopulation analyses are handled with meta.best.cis.eQTLs and meta.transScores. o High volume genotype data has been addressed by packaging ExpressionSet and chromosome-specific SnpMatrix instances; requests for expression plus genotype data are directed to packages mediated through GGBase::getSS. o Two species of data filtering parameters that may be used jointly in the primary tools are exFilter, which operates on expression component prior to any analyses, and smFilter, which operates on the entire smlSet. exFilter may be used to isolate samples of interest early in the workflow, for example when an expression plus genotype package includes samples from distinct tissues on the same individuals. o june 2012: exFilter facility properly handled in best.cis.eQTLs.mchr o may 2012: best.cis.eQTLs has getDFFITS option o march 2010: gwSnpTests and so forth are deprecated in favor of simpler interfaces that can be more readily parallelized. New IRanges-based computations for cis restrictions will be introduced CHANGES IN VERSION 3.0 ---------------------- o march 2008: complete overhaul to use snpMatrix genotype representation. gwSnpScreen is main interface o manage warnings of ff.[ a bit better, May 13 2012 o racExSet is not a primary tool any more; smlSet is