Convert other data formats to linkSet. Currently supported: GInteractions, data.frame.
Usage
# S4 method for class 'GInteractions'
Convert(x, baitCol = NULL, ...)
# S4 method for class 'data.frame'
Convert(x, source = "data.frame", baitCol = "gene", oeCol = "peak", ...)
# S4 method for class 'Pairs'
Convert(x, baitCol = NULL, ...)
# S4 method for class 'ANY'
Convert(x, baitCol = NULL, ...)
readvalidPairs(file, njobs = 1, format = "validPairs")Arguments
- x
An object of unsupported class
- baitCol
A character string specifying the column to use for bait naming
- ...
Additional arguments (not used)
- source
The source of the data frame, either "data.frame" or "chicane"
- oeCol
The column name in the data frame that contains the other end information
- file
A character string specifying the path to the validPairs file or 4DN pairs file
- njobs
An integer specifying the number of threads to use for reading the file
- format
A character string specifying the format of the file, either "validPairs" or "pair". Pair format should be "readID chr1 pos1 chr2 pos2 strand1 strand2". And validPairs should be "readID chr1 pos1 strand1 chr2 pos2 strand2".
Value
A linkSet object
A linkSet object
A linkSet object
Nothing, throws an error
A GInteractions object
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
#>
#> Attaching package: ‘InteractionSet’
#> The following objects are masked from ‘package:linkSet’:
#>
#> anchorIds, anchors, pairdist, reduceRegions, regions, regions<-
gi <- GInteractions(anchor1 = c(1, 2), anchor2 = c(3, 4), regions = GRanges(seqnames = c("chr1", "chr1", "chr2", "chr2"),
ranges = IRanges(start = c(100, 200, 300, 400), width = 50)))
ls <- Convert(gi)
ls
#> linkSet object with 2 interactions and 0 metadata columns:
#> bait seqnames_oe ranges_oe
#> <character> <Rle> <IRanges>
#> [1] chr1:100-149 --- chr2 300-349
#> [2] chr1:200-249 --- chr2 400-449
#> -------
#> regions: 4 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
df <- data.frame(
gene = c("gene1", "gene2"),
peak = c("chr1:1000-2000", "chr2:1500-2500"),
score = c(5.5, 6.0)
)
ls <- Convert(df, source = "data.frame", baitCol = "gene", oeCol = "peak")
ls
#> linkSet object with 2 interactions and 1 metadata column:
#> bait seqnames_oe ranges_oe | score
#> <character> <Rle> <IRanges> | <numeric>
#> [1] gene1 --- chr1 1000-2000 | 5.5
#> [2] gene2 --- chr2 1500-2500 | 6.0
#> -------
#> regions: 2 ranges and 0 metadata columns
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths