GInteractions operator

GInteractions operations (add, aubtract, multiply, divide)

GIoperator(gi_list, col = "score", operator = c("+", "-", "*", "/"))

Arguments

gi_list

a list of GInteractions objects

col

colname of metadata to be calculated

operator

operator, "+" means A + B, and so on. User-defined function also could be used.

Value

an object of GInteractions

Examples

library(InteractionSet)
#> Loading required package: SummarizedExperiment
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#> 
#> Attaching package: 'MatrixGenerics'
#> The following objects are masked from 'package:matrixStats':
#> 
#>     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#>     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#>     colWeightedMeans, colWeightedMedians, colWeightedSds,
#>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#>     rowWeightedSds, rowWeightedVars
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> Attaching package: 'Biobase'
#> The following object is masked from 'package:MatrixGenerics':
#> 
#>     rowMedians
#> The following objects are masked from 'package:matrixStats':
#> 
#>     anyMissing, rowMedians
gr2 <- GRanges(seqnames=c("chr1", "chr1"),
               ranges=IRanges(c(7,13), width=3))
gr3 <- GRanges(seqnames=c("chr1", "chr1"),
               ranges=IRanges(c(1, 4), c(3, 9)))
gi <- GInteractions(gr2, gr3, score=c(1, 2))
gi2 <- GInteractions(gr2, gr3, score=c(3, 4))
GIoperator(list(gi, gi2), col="score", operator="+")
#> GInteractions object with 2 interactions and 1 metadata column:
#>       seqnames1   ranges1     seqnames2   ranges2 |     score
#>           <Rle> <IRanges>         <Rle> <IRanges> | <numeric>
#>   [1]      chr1       7-9 ---      chr1       1-3 |         4
#>   [2]      chr1     13-15 ---      chr1       4-9 |         6
#>   -------
#>   regions: 4 ranges and 0 metadata columns
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
GIoperator(list(gi, gi2), col="score", operator="-")
#> GInteractions object with 2 interactions and 1 metadata column:
#>       seqnames1   ranges1     seqnames2   ranges2 |     score
#>           <Rle> <IRanges>         <Rle> <IRanges> | <numeric>
#>   [1]      chr1       7-9 ---      chr1       1-3 |        -2
#>   [2]      chr1     13-15 ---      chr1       4-9 |        -2
#>   -------
#>   regions: 4 ranges and 0 metadata columns
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths