## ----setup, include=FALSE--------------------------------------------------------------------------------------------- options(width=120) knitr::opts_chunk$set( echo=TRUE ) ## ---- eval=FALSE------------------------------------------------------------------------------------------------------ # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("pgca") ## --------------------------------------------------------------------------------------------------------------------- library(pgca) ## --------------------------------------------------------------------------------------------------------------------- head(BET2007_v339) ## --------------------------------------------------------------------------------------------------------------------- subset(BET2007_v339, N %in% N[Gene_Symbol == 'PRSS2']) ## --------------------------------------------------------------------------------------------------------------------- subset(BET2047_v339, N %in% N[Gene_Symbol == 'PRSS2']) ## --------------------------------------------------------------------------------------------------------------------- dict <- pgcaDict( BET2007_v339, BET2047_v339, col.mapping=c(gene.symbol="Gene_Symbol") ) ## --------------------------------------------------------------------------------------------------------------------- dict ## --------------------------------------------------------------------------------------------------------------------- subset(dict$dictionary, pg %in% pg[gene == 'PRSS2']) ## --------------------------------------------------------------------------------------------------------------------- translated <- applyDict(BET2007_v339, BET2047_v339, dict=dict) ## --------------------------------------------------------------------------------------------------------------------- subset(translated$BET2007_v339, Gene_Symbol == "PRSS2") subset(translated$BET2047_v339, Gene_Symbol == "PRSS2") ## --------------------------------------------------------------------------------------------------------------------- dict.from.files <- pgcaDict( system.file("extdata", "BET1947_v339.txt", package="pgca"), system.file("extdata", "BET2007_v339.txt", package="pgca"), system.file("extdata", "BET2047_v339.txt", package="pgca"), system.file("extdata", "BET2067_v339.txt", package="pgca"), col.mapping=c(gene.symbol="Gene_Symbol") ) dict.from.files ## --------------------------------------------------------------------------------------------------------------------- dict.from.dir <- pgcaDict( system.file("extdata", package="pgca"), col.mapping=c(gene.symbol="Gene_Symbol") ) dict.from.dir ## --------------------------------------------------------------------------------------------------------------------- subset(dict.from.dir$dictionary, pg %in% pg[gene == "PRSS2"]) ## --------------------------------------------------------------------------------------------------------------------- translated2 <- applyDict(BET1947_v339, BET2007_v339, BET2047_v339, BET2067_v339, dict=dict.from.dir) ## --------------------------------------------------------------------------------------------------------------------- subset(translated2$BET1947_v339, Gene_Symbol == 'PRSS2') subset(translated2$BET2007_v339, Gene_Symbol == 'PRSS2') ## --------------------------------------------------------------------------------------------------------------------- dictOutFile <- tempfile() saveDict(dict.from.dir, file=dictOutFile) ## ---- echo=FALSE, results='asis'-------------------------------------------------------------------------------------- cat('[1]') print(readCitationFile("../inst/CITATION"), style = "text")