lost
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LOST. in the genome… f ind where you at, fool!. Nirav Malani Rick Bushman Lab Department of Microbiology University of Pennsylvania. Basic Idea: “ Know Your Surroundings”. Where is the concept coming from? Retrovirus integration pattern What are you trying to deduce? - PowerPoint PPT PresentationTRANSCRIPT
LOST
Nirav Malani
Rick Bushman LabDepartment of MicrobiologyUniversity of Pennsylvania
in the genome…find where you at,
fool!
Basic Idea:“Know Your Surroundings”
Where is the concept coming from? Retrovirus integration pattern
What are you trying to deduce? Sense of genomic environment and/or
preferences
What kind of data are you analyzing? Genomic coordinates from some species
hiAnnotator R package to annotate genomic ranges Fundamentals
Take two RangedData objects (query & subject)
Call a specific annotation type function Define customization parameters…optional. That’s it!
Depends On: IRanges, doBy
Prepare the Objects> head(sites)
> makeRangedData(sites,soloStart=TRUE)
Prepare the Objects> head(genes)
> makeRangedData(genes)
Usage: makeRangedData(x, positionsOnly=FALSE, soloStart=FALSE, chromCol=NULL, strandCol=NULL, startCol=NULL, stopCol=NULL)
Annotation TypesIN/OUT
Usage: getSitesInFeature(sites.rl, genes.rl, “InGene”)
Annotation TypesIN/OUT
Usage: getSitesInFeature(sites.rl, genes.rl, “InGene”, asBool=T)
Annotation TypesNEAREST
Usage: getNearestFeature(sites.rl, genes.rl, “NearestGene”)
Annotation TypesFEATURE COUNTS
Usage: getFeatureCounts( sites.rl, genes.rl, “NumOfGene”,chromSizes = seqlengths(Hsapiens))
Preliminary Analysis
Preliminary Analysis
In Works Parallel backend support for all the functions Function for GC% annotation
That’s It!