# infrastructure for genetics of gene expression (c) 2008 VJ Carey

## Documentation for package ‘GGBase’ version 2.0.4

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

chrnum | Class "genesym" and other casting classes
chrnum,numeric-method | Class "genesym" and other casting classes
chrnum-class | Class "genesym" and other casting classes
cnumOrMissing | Class "genesym" and other casting classes
cnumOrMissing-class | Class "genesym" and other casting classes
cwSnpScreenResult-class | Class "gwSnpScreenResult" - container for GGtools gwSnpScreen method outputs and allied objects
exFeatID | Class "genesym" and other casting classes
exFeatID-class | Class "genesym" and other casting classes
genesym | Class "genesym" and other casting classes
genesym-class | Class "genesym" and other casting classes
GGfitter-class | Class "GGfitter" legacy container for fast fitting of eQTL search models - obsolete, see gwSnpScreen for more current approaches
gwSnpScreenResult-class | Class "gwSnpScreenResult" - container for GGtools gwSnpScreen method outputs and allied objects
hmceuAmbB36_23a_dbconn | SQLite infrastructure for SNP locations
hmceuAmbB36_23a_dbfile | SQLite infrastructure for SNP locations
initialize,racExSet-method | Class "racExSet" - container for genotype data in 'rare allele count' form and expression data. Approaching obsolescence, see smlSet for more efficient representation.
multiGwSnpScreenResult-class | Class "gwSnpScreenResult" - container for GGtools gwSnpScreen method outputs and allied objects
oGtypeExSet-class | Class "oGtypeExSet" oligo-based genotyping output + expression set container - obsolete
racExSet-class | Class "racExSet" - container for genotype data in 'rare allele count' form and expression data. Approaching obsolescence, see smlSet for more efficient representation.
rsNum | Class "genesym" and other casting classes
rsNum,character-method | Class "genesym" and other casting classes
rsNum-class | Class "genesym" and other casting classes
show,snpLocNCref-method | Class "genesym" and other casting classes
smlEnv | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes
smlEnv,smlSet-method | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes
smList | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes
smList,smlSet-method | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes
smlSet-class | Documentation on S4 class "smlSet" an eSet-derived container for snpMatrix lists, allowing efficient combination of SNP chip genotyping with microarray expression data, and allied classes
snpID | Class "genesym" and other casting classes
snpID-class | Class "genesym" and other casting classes
snpLocNCref | Class "genesym" and other casting classes
snpLocNCref-class | Class "genesym" and other casting classes
snpMeta-class | Class "snpMeta" representing SNP locations etc., obsolete for humans, still used for murine data.
snpMetaWhole-class | Class "snpMeta" representing SNP locations etc., obsolete for humans, still used for murine data.
snpScreenResult-class | Class "snpScreenResult" - container approaching obsolescence, retained for legacy purposes, that holds expression vs genotype analysis results; see gwSnpScreenResult for more current approach.
twSnpScreenResult-class | Class "snpScreenResult" - container approaching obsolescence, retained for legacy purposes, that holds expression vs genotype analysis results; see gwSnpScreenResult for more current approach.