## ----setup, include=FALSE, cache=FALSE---------------------------------------- library(knitr) # set global chunk options opts_chunk$set(concordance=TRUE) ## ----options,echo=FALSE----------------------------------- options(width=60) ## ----Genomic Features------------------------------------- library(Guitar) # genomic features imported into named list stBedFiles <- list(system.file("extdata", "m6A_mm10_exomePeak_1000peaks_bed12.bed", package="Guitar")) ## ----label=quick_plot,eval=FALSE-------------------------- # count <- GuitarPlot(txGenomeVer = "mm10", # stBedFiles = stBedFiles, # miscOutFilePrefix = NA) # ## ----Guitar coordiantes----------------------------------- txdb_file <- system.file("extdata", "mm10_toy.sqlite", package="Guitar") txdb <- loadDb(txdb_file) guitarTxdb <- makeGuitarTxdb(txdb = txdb, txPrimaryOnly = FALSE) # Or use gff. file to generate guitarTxdb # Or use getTxdb() to download TxDb from internet: # txdb <- getTxdb(txGenomeVer="hg19") # guitarTxdb <- makeGuitarTxdb(txdb) ## ----label=example,echo=TRUE,fig.height=6,fig.width=12---- GuitarPlot(txTxdb = txdb, stBedFiles = stBedFiles, miscOutFilePrefix = "example") ## ----label=parameter_1,echo=TRUE,fig.height=6,fig.width=12---- GuitarPlot(txTxdb = txdb, stBedFiles = stBedFiles, headOrtail = TRUE) ## ----label=parameter_2,echo=TRUE,fig.height=6,fig.width=12---- GuitarPlot(txTxdb = txdb, stBedFiles = stBedFiles, headOrtail = TRUE, enableCI = FALSE) ## ----label=mm10_example,echo=TRUE,fig.height=6,fig.width=12---- # import different data formats into a named list object. # These genomic features are using mm10 genome assembly stBedFiles <- list(system.file("extdata", "m6A_mm10_exomePeak_1000peaks_bed12.bed", package="Guitar"), system.file("extdata", "m6A_mm10_exomePeak_1000peaks_bed6.bed", package="Guitar")) # Build Guitar Coordinates txdb_file <- system.file("extdata", "mm10_toy.sqlite", package="Guitar") txdb <- loadDb(txdb_file) # Guitar Plot GuitarPlot(txTxdb = txdb, stBedFiles = stBedFiles, headOrtail = TRUE, enableCI = FALSE, mapFilterTranscript = TRUE, pltTxType = c("mrna"), stGroupName = c("BED12","BED6")) ## ----label=sample,echo=TRUE,fig.height=6,fig.width=12----- stGRangeLists = vector("list", length(stBedFiles)) sitesPoints <- list() for (i in seq_len(length(stBedFiles))) { stGRangeLists[[i]] <- blocks(import(stBedFiles[[i]])) } for (i in seq_len(length(stGRangeLists))) { sitesPoints[[i]] <- samplePoints(stGRangeLists[i], stSampleNum = 10, stAmblguity = 5, pltTxType = c("mrna"), stSampleModle = "Equidistance", mapFilterTranscript = FALSE, guitarTxdb = guitarTxdb) } ## ----label=GuitarTxdb,eval=TRUE--------------------------- guitarTxdb <- makeGuitarTxdb(txdb = txdb, txAmblguity = 5, txMrnaComponentProp = c(0.1,0.15,0.6,0.05,0.1), txLncrnaComponentProp = c(0.2,0.6,0.2), pltTxType = c("tx","mrna","ncrna"), txPrimaryOnly = FALSE) ## ----label=Check,echo=TRUE,fig.height=6,fig.width=12------ gcl <- list(guitarTxdb$tx$tx) GuitarPlot(txTxdb = txdb, stGRangeLists = gcl, stSampleNum = 200, enableCI = TRUE, pltTxType = c("tx"), txPrimaryOnly = FALSE ) ## ----label=tx_comp,eval=TRUE------------------------------ GuitarCoords <- guitarTxdb$tx$txComponentGRange type <- paste(mcols(GuitarCoords)$componentType,mcols(GuitarCoords)$txType) key <- unique(type) landmark <- list(1,2,3,4,5,6,7,8,9,10,11) names(landmark) <- key for (i in 1:length(key)) { landmark[[i]] <- GuitarCoords[type==key[i]] } GuitarPlot(txTxdb = txdb , stGRangeLists = landmark[1:3], pltTxType = c("tx"), enableCI = FALSE ) ## ----label=mrna_comp,eval=TRUE---------------------------- GuitarPlot(txTxdb = txdb , stGRangeLists = landmark[4:8], pltTxType = c("mrna"), enableCI = FALSE ) ## ----label=comp,eval=TRUE--------------------------------- GuitarPlot(txTxdb = txdb , stGRangeLists = landmark[9:11], pltTxType = c("ncrna"), enableCI = FALSE ) ## ----label=session,eval=TRUE------------------------------ sessionInfo()