Guitar-package {Guitar} | R Documentation |
RNA Landmarks Guided Transcriptomic View of RNA-related Genomic Features.
The package is designed for transcriptomic visualization of RNA-related genomic features represented with genome-based coordinates with respect to the landmarks of RNA transcripts, i.e., transcription starting site, start codon, stop codon and transcription ending site.
Jia Meng <jia.meng@hotmail.com>
~~ Literature or other references for background information ~~
# read genomic features narrowPeak <- system.file( "extdata", "m6A_hg19_1000peaks_macs2.narrowPeak", package="Guitar") # bam imported as GAlignments m6A_Bcell <- narrowPeaktoGRanges(narrowPeak) # generate a list of genomic features m6A_Bcell_1 <- m6A_Bcell[1:300] m6A_Bcell_2 <- m6A_Bcell[301:600] m6A_Bcell_3 <- m6A_Bcell[601:900] feature_hg19 <- list(m6A_Bcell_1, m6A_Bcell_2, m6A_Bcell_3) names(feature_hg19) <- c("m6A_1","m6A_2","m6A_3") # Make Guitar coordiantes txdb_file <- system.file("extdata", "hg19_toy.sqlite", package="Guitar") txdb <- loadDb(txdb_file) gc_txdb <- makeGuitarCoordsFromTxDb(txdb,noBins =10) # Plot GuitarPlot(feature_hg19, GuitarCoordsFromTxDb = gc_txdb)