Guitar-package {Guitar} | R Documentation

## Guitar

### Description

RNA Landmarks Guided Transcriptomic View of RNA-related Genomic Features.

### Details

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.

### Author(s)

Jia Meng <jia.meng@hotmail.com>

### References

~~ Literature or other references for background information ~~

### Examples

    # 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)

[Package Guitar version 1.18.0 Index]