inst/doc/ggbase.R

In GGBase: GGBase infrastructure for genetics of gene expression package GGtools

## ----lkc----------------------------------------------------------------------
library(GGBase)
getClass("smlSet")
showMethods(class="smlSet", where="package:GGBase")

## ----lkd----------------------------------------------------------------------
if ("GGtools" %in% installed.packages()[,1]) {
 library(GGtools)
 s20 = getSS("GGtools", "20")
 s20
}

## ----lkf,fig=TRUE-------------------------------------------------------------
if (exists("s20")) {
 plot_EvG(genesym("CPNE1"), rsid("rs6060535"), s20)
} else plot(1) # pdf must exist....

## ----lkgt,keep.source=TRUE----------------------------------------------------
if (exists("s20")) {
# raw bytes
 as(smList(s20)[[1]], "matrix")[1:5,1:5]
# generic calls
 as(smList(s20)[[1]], "character")[1:5,1:5]
# risk allele (alphabetically later nucleotide) counts
 as(smList(s20)[[1]], "numeric")[1:5,1:5]
}