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!
