makeGInteractionsFromDataFrame.RdmakeGInteractionsFromDataFrame takes a paired-interaction (i.e. BEDPE) formatted data-frame-like object and converts it to a GInteractions object. For convenience, as_ginteractions() can be used as an alias.
makeGInteractionsFromDataFrame(
df,
keep.extra.columns = TRUE,
starts.in.df.are.0based = FALSE
)
as_ginteractions(
df,
keep.extra.columns = TRUE,
starts.in.df.are.0based = FALSE
)A data.table, data.frame, or DataFrame object. Assumes that the first 6 colummns are in the format chr1, start1, end1 and chr2, start2, end2, representing each pair of interactions.
TRUE or FALSE (the default). If TRUE, the columns in df that are not used to form the genomic ranges of the returned GRanges object are then returned as metadata columns on the object. Otherwise, they are ignored. If df has a width column, then it's always ignored.
TRUE or FALSE (the default). If TRUE, then the start positions of the genomic ranges in df are considered to be 0-based and are converted to 1-based in the returned GRanges object. This feature is intended to make it more convenient to handle input that contains data obtained from resources using the "0-based start" convention. A notorious example of such resource is the UCSC Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables).
GInteraction object
## data.frame
df <- data.frame(chr1 = "chr1", x1 = 10000, x2 = 20000,
chr2 = "chr1", y1 = 30000, y2 = 40000)
makeGInteractionsFromDataFrame(df)
#> GInteractions object with 1 interaction and 0 metadata columns:
#> seqnames1 ranges1 seqnames2 ranges2
#> <Rle> <IRanges> <Rle> <IRanges>
#> [1] chr1 10000-20000 --- chr1 30000-40000
#> -------
#> regions: 2 ranges and 0 metadata columns
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## data.table
df <- data.table(chr1 = "chr1", x1 = 10000, x2 = 20000,
chr2 = "chr1", y1 = 30000, y2 = 40000)
#> Error in data.table(chr1 = "chr1", x1 = 10000, x2 = 20000, chr2 = "chr1", y1 = 30000, y2 = 40000): could not find function "data.table"
makeGInteractionsFromDataFrame(df)
#> GInteractions object with 1 interaction and 0 metadata columns:
#> seqnames1 ranges1 seqnames2 ranges2
#> <Rle> <IRanges> <Rle> <IRanges>
#> [1] chr1 10000-20000 --- chr1 30000-40000
#> -------
#> regions: 2 ranges and 0 metadata columns
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## DataFrame
df <- DataFrame(chr1 = "chr1", x1 = 10000, x2 = 20000,
chr2 = "chr1", y1 = 30000, y2 = 40000)
makeGInteractionsFromDataFrame(df)
#> GInteractions object with 1 interaction and 0 metadata columns:
#> seqnames1 ranges1 seqnames2 ranges2
#> <Rle> <IRanges> <Rle> <IRanges>
#> [1] chr1 10000-20000 --- chr1 30000-40000
#> -------
#> regions: 2 ranges and 0 metadata columns
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## Alias
df <- data.frame(chr1 = "chr1", x1 = 10000, x2 = 20000,
chr2 = "chr1", y1 = 30000, y2 = 40000,
pval = 0.05, dist = 10000)
as_ginteractions(df)
#> GInteractions object with 1 interaction and 2 metadata columns:
#> seqnames1 ranges1 seqnames2 ranges2 | pval dist
#> <Rle> <IRanges> <Rle> <IRanges> | <numeric> <numeric>
#> [1] chr1 10000-20000 --- chr1 30000-40000 | 0.05 10000
#> -------
#> regions: 2 ranges and 0 metadata columns
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## Additional metadata
df <- data.frame(chr1 = "chr1", x1 = 10000, x2 = 20000,
chr2 = "chr1", y1 = 30000, y2 = 40000,
pval = 0.05, dist = 10000)
as_ginteractions(df)
#> GInteractions object with 1 interaction and 2 metadata columns:
#> seqnames1 ranges1 seqnames2 ranges2 | pval dist
#> <Rle> <IRanges> <Rle> <IRanges> | <numeric> <numeric>
#> [1] chr1 10000-20000 --- chr1 30000-40000 | 0.05 10000
#> -------
#> regions: 2 ranges and 0 metadata columns
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## Remove additional metadata
as_ginteractions(df, keep.extra.columns = F)
#> GInteractions object with 1 interaction and 0 metadata columns:
#> seqnames1 ranges1 seqnames2 ranges2
#> <Rle> <IRanges> <Rle> <IRanges>
#> [1] chr1 10000-20000 --- chr1 30000-40000
#> -------
#> regions: 2 ranges and 0 metadata columns
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## Add 1 to starts (for 0-based programs)
as_ginteractions(df, starts.in.df.are.0based = T)
#> GInteractions object with 1 interaction and 2 metadata columns:
#> seqnames1 ranges1 seqnames2 ranges2 | pval dist
#> <Rle> <IRanges> <Rle> <IRanges> | <numeric> <numeric>
#> [1] chr1 10001-20000 --- chr1 30001-40000 | 0.05 10000
#> -------
#> regions: 2 ranges and 0 metadata columns
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## Bad usage
df <- data.frame(chr1 = "chr1", x1 = 10000, x2 = 20000,
chr2 = "chr1", y1 = 30000)
makeGInteractionsFromDataFrame(df)
#> Error in makeGInteractionsFromDataFrame(df): ncol(df) must be >= 6 and start with paired interactions (i.e. chr1, start1, end1 and chr2, start2, end2).