## ----include=FALSE,cache=FALSE------------------------------------------------ library(codelink) library(knitr) opts_chunk$set(fig.align = 'center', concordance=TRUE) ## ----input, eval=FALSE-------------------------------------------------------- # # NOT RUN # # library(codelink) # foo <- readCodelink() # summaryFlag(foo) # will show a summary of flag values. # # NOT RUN # ## ----data, comment=NA--------------------------------------------------------- data(codelink.example) codelink.example ## ----input-flag, eval=FALSE--------------------------------------------------- # foo <- readCodelink(flag = list(M = 0.01) ) ## ----bkgcorrect, eval=FALSE--------------------------------------------------- # foo <- bkgdCorrect(foo, method = "half") ## ----normalize, eval=FALSE---------------------------------------------------- # foo <- normalize(foo, method = "quantiles") ## ----plotMA------------------------------------------------------------------- plotMA(codelink.example) ## ----plotDensity-------------------------------------------------------------- plotDensities(codelink.example) ## ----image, eval=FALSE-------------------------------------------------------- # imageCodelink(foo) # imageCodelink(foo, what = "snr") ## ----merge, eval=FALSE-------------------------------------------------------- # foo <- mergeArray(foo, class = c(1, 1, 2, 2), names = c("A", "B")) # plotCV(foo) ## ----read-fix, eval=FALSE----------------------------------------------------- # foo <- readCodelink(fix = TRUE) ## ----read-codelinkSet, eval=FALSE--------------------------------------------- # foo <- readCodelinkSet()