Illumina data

Description Usage Arguments Value See Also Examples

Given a group of discrete factors (i.e. position ids) and integer values, the function tests if they overlap between groups. If overlap is found, then the group having highest frequency of a given position wins, else the position is filtered out from all the groups. The main use of this function is to remove crossover sites from different samples in the data.

1 2	crossOverCheck(posID = NULL, value = NULL, grouping = NULL, weight = NULL, windowSize = 1, psl.rd = NULL)

`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.
`grouping`	additional vector of grouping of length posID or psl.rd by which to pool the rows (i.e. samplenames). Default is NULL.
`weight`	a numeric vector of weights to use when calculating frequency of value by posID and grouping if specified. Default is NULL.
`windowSize`	size of window within which values should be checked. Default is 1.
`psl.rd`	a GRanges object. Default is NULL.

a data frame of the original input with columns denoting whether a given row was a Candidate and isCrossover. If psl.rd parameter is defined, then a GRanges object with 'isCrossover', 'Candidate', and 'FoundIn' columns appended at the end.

clusterSites, otuSites, findIntegrations, getIntegrationSites, pslToRangedObject

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crossOverCheck(posID = c('chr1-', 'chr1-', 'chr1-', 'chr1-', 'chr2+', 'chr15-', 
'chr16-', 'chr11-'), value = c(rep(1000, 3), 5832, 1000, 12324, 65738, 928042), 
grouping = c('a', 'a', 'b', 'b', 'b', 'b', 'c', 'c'))