condense_intsites: Condense integration site GRanges to distinct genomic...
In cnobles/gintools: Genomic DNA Integration Analysis Tools

Description Usage Arguments Details Author(s) Examples

Given a GRanges object representing the genomic ranges of sequenced DNA flanking the viral/vector integrating site, this function returns only the distinct integration site positions. Further, using the options for return.abundance and method, the function can return abundance or estimated abundance information based on fragment length (see sonicLength package). Initial GRanges object can carry multiple samples which can be separated and analyzed independently by using the grouping option.

condense_intsites(sites.to.condense)

condense_intsites(sites.to.condense, grouping = NULL,
return.abundance = FALSE, method = "fragLen", replicates = "replicates")

`sites.to.condense`	a GRanges object where each row represents a genomic range of reference genome DNA.
`grouping`	metadata column name (input as character) which designates which genomic ranges belong to which sample.
`return.abundance`	logical that will subject the data to abundance calculations, default is FALSE.
`method`	either "fragLen" (default) or "estAbund" to be passed to determine_abundance function. method = "fragLen" determines the abundance by the number of unique genomic ranges widths while the method = "estAbund" utilizes the sonicLength package.
`replicates`	character name of the column carrying the replicate information, relevant for abundance calculations and irrelent after using the this function.
`quiet`	logical indicating if output message should be displayed.

condense_intsites condenses or collapses GRanges data to distinct integration positions in the reference genome.

Christopher Nobles, Ph.D.

gr <- gintools:::generate_test_granges()
std.gr <- standardize_sites(gr)
condense_intsites(std.gr)

condense_intsites(std.gr, return.abundance = TRUE)