isuSites: Bin values or make ISUs by assigning a unique ID to them...
In hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data

Description Usage Arguments Value Note See Also Examples

Given a group of values or genomic positions per read/clone, the function tries to yield a unique ISU (Integration Site Unit) ID for the collection based on overlap of locations to other reads/clones by grouping. This is mainly useful when each read has many locations which needs to be considered as one single group of sites.

1 2	isuSites(posID = NULL, value = NULL, readID = NULL, grouping = NULL, psl.rd = NULL, maxgap = 5, parallel = TRUE)

`posID`	a vector of groupings for the value parameter (i.e. Chr,strand). Required if psl.rd parameter is not defined.
`value`	a vector of integer locations/positions that needs to be binned, i.e. genomic location. Required if psl.rd parameter is not defined.
`readID`	a vector of read/clone names which is unique to each row, i.e. deflines.
`grouping`	additional vector of grouping of length posID or psl.rd by which to pool the rows (i.e. samplenames). Default is NULL.
`psl.rd`	a GRanges object returned from `clusterSites`. Default is NULL.
`maxgap`	max distance allowed between two non-overlapping position to trigger the merging. Default is 5.
`parallel`	use parallel backend to perform calculation with `BiocParallel`. Defaults to TRUE. If no parallel backend is registered, then a serial version is ran using `SerialParam`. Process is split by the grouping the column.

a data frame with binned values and isuID shown alongside the original input. If psl.rd parameter is defined, then a GRanges object where object is first filtered by clusterTopHit column and the isuID column appended at the end.

The algorithm for making isus of sites is as follows: for each readID check how many positions are there. Separate readIDs with only position from the rest. Check if any readIDs with >1 position match to any readIDs with only one position. If there is a match, then assign both readIDs with the same ISU ID. Check if any positions from readIDs with >1 position match any other readIDs with >1 position. If yes, then assign same ISU ID to all readIDs sharing 1 or more positions.

clusterSites, isuSites, crossOverCheck, findIntegrations, getIntegrationSites, pslToRangedObject

isuSites(posID = c('chr1-', 'chr1-', 'chr1-', 'chr2+', 'chr15-', 'chr16-', 'chr11-'), 
value = c(rep(1000, 2), 5832, 1000, 12324, 65738, 928042), 
readID = paste('read', sample(letters, 7), sep = '-'), 
grouping = c('a', 'a',  'a', 'b', 'b', 'b', 'c'), parallel = FALSE)