srnadiffExample: Example constructor

In mzytnicki/srnadiff: Finding differentially expressed unannotated genomic regions from RNA-seq data

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

mzytnicki/srnadiff documentation built on March 7, 2023, 2:18 a.m.