rice.bg {vasp} | R Documentation

## Rice Ballgown Object

### Description

Small ballgown object created with a subset of rice RNAseq data, for demonstration purposes

### Usage

    rice.bg

### Format

a ballgown object with 33 transcripts and 6 samples

### Details

The raw RNA-seq data were screened and trimmed using Trimmomatic (Bolger et al., 2014) and RNA-seq mapping, transcript assembly, and quantification were conducted with HISAT, StringTie, and Ballgown by following the method described by Pertea et al. (Pertea et al., 2016). The rice.bg is a subset ballgown object with 33 transcripts and 6 samples. #> library(vasp) #> ?ballgown #> path<-system.file('extdata', package='vasp') #> rice.bg<-ballgown(samples = list.dirs(path = path,recursive = F))

### Source

The raw RNA-seq data were from the project of variation in transcriptional responses to salt stress in rice (SRA Accession: SRP106054).

### References

Bolger, A.M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120.

Pertea, M., Kim, D., Pertea, G.M., Leek, J.T., and Salzberg, S.L. (2016). Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc 11, 1650-1667.

### Examples

    data(rice.bg)
    rice.bg
    # ballgown instance with 33 transcripts and 6 samples

[Package vasp version 1.0.0 Index]