isuSites: Bin values or make ISUs by assigning a unique ID to them...

Description Usage Arguments Value Note See Also Examples

View source: R/hiReadsProcessor.R


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.


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



a vector of groupings for the value parameter (i.e. Chr,strand). Required if psl.rd parameter is not defined.


a vector of integer locations/positions that needs to be binned, i.e. genomic location. Required if psl.rd parameter is not defined.


a vector of read/clone names which is unique to each row, i.e. deflines.


additional vector of grouping of length posID or psl.rd by which to pool the rows (i.e. samplenames). Default is NULL.


a GRanges object returned from clusterSites. Default is NULL.


max distance allowed between two non-overlapping position to trigger the merging. Default is 5.


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.

See Also

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)

hiReadsProcessor documentation built on Nov. 8, 2020, 5:43 p.m.