srnadiffExample {srnadiff} | R Documentation

## Example constructor

### Description

This function provides an example of a `srnadiffExp` object which contains mapped reads of small RNAs extracted from SLK cells infected with latent KSHV, compared to uninfected SLK cells.

### Usage

    srnadiffExample()

### Details

Raw data have been downloaded from the GEO data set GSE62830, provided in Viollet et al. (2015). Adapters were removed with fastx_clipper and mapped with bowtie2 (Salzberg and Langmead, 2012) on the human genome version GRCh38.

This example is restricted to a small locus on chr14. It uses the whole genome annotation (with coding genes, etc.) and extracts miRNAs.

### Value

An `srnadiffExp` object called '`srnaExp`'.

### References

Viollet, Coralie, David A. Davis, Martin Reczko, Joseph M. Ziegelbauer, Francesco Pezzella, Jiannis Ragoussis, and Robert Yarchoan (2015). "Next-Generation Sequencing Analysis Reveals Differential Expression Profiles of MiRNA-mRNA Target Pairs in KSHV-Infected Cells." PLOS ONE, 10:1–23.

Salzberg, Steven, and Ben Langmead (2012). "Fast gapped-read alignment with Bowtie 2." Nature Methods, 9:357–59.

### Examples

    ## The 'srnadiffExp' object in this example was constructed by:

    ## Not run:

    basedir             <- system.file("extdata", package="srnadiff", mustWork = TRUE)
    sampleInfo          <- read.csv(file.path(basedir, "dataInfo.csv"))
    gtfFile             <- file.path(basedir, "Homo_sapiens.GRCh38.76.gtf.gz")
    annotReg            <- readAnnotation(gtfFile, feature="gene", source="miRNA")
    bamFiles            <- file.path(basedir, sampleInfo$FileName)
    srnaExp             <- srnadiffExp(bamFiles, sampleInfo, annotReg)
    parameters(srnaExp) <- srnadiffDefaultParameters
    save(srnaExp, file = file.path(basedir, "srnadiffExample.rda"))

    ## End(Not run)

    srnaExp <- srnadiffExample()
    srnaExp

[Package srnadiff version 1.14.0 Index]