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.
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.
srnadiffExp object called '
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.
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## 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 <- paste(file.path(basedir, sampleInfo$FileName), "bam", sep=".") srnaExp <- srnadiffExp(bamFiles, sampleInfo, annotReg) ## End(Not run) srnaExp <- srnadiffExample() srnaExp
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