otuSites: Bin values or make OTUs 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 OTU (operation taxinomical 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	otuSites(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 otuID shown alongside the original input. If psl.rd parameter is defined, then a GRanges object.

The algorithm for making OTUs of sites is as follows:

for each grouping & posID, fix values off by maxgap parameter
create bins of fixed values per readID
assign arbitrary numeric ID to each distinct bins above & obtain its frequency
perform overlap b/w readIDs with only one value (singletons) to readIDs with >1 value (non-singletons)
- for any overlapping values, tag non-singleton readID with the ID of singleton readID
- if non-singleton readID matched with more than one singleton readID, then pick on at random
for any non-tagged & non-singleton readIDs, perform an overlap of values within themselves using the maxgap parameter
- tag any overlapping positions across any readID with the ID of most frequently occuring bin
positions with no overlap are left as is with the original arbitrary ID

clusterSites, isuSites, crossOverCheck, findIntegrations, getIntegrationSites, pslToRangedObject

otuSites(posID = c('chr1-', 'chr1-', 'chr1-', 'chr2+', 'chr15-', 'chr16-', 'chr11-'),
value = c(1000, 1003, 5832, 1000, 12324, 65738, 928042), 
readID = paste('read', sample(letters, 7), sep = '-'), 
grouping = c('a', 'a', 'a', 'b', 'b', 'b', 'c'), parallel = FALSE)