Add gaps between GRangesList regions

addGRLgaps(
  grl,
  strandSpecific = TRUE,
  gapname = "gap",
  suffix = "_v",
  newValues = list(feature_type = "gap"),
  default_feature_type = "exon",
  feature_type_colname = "feature_type",
  doSort = TRUE,
  verbose = FALSE,
  ...
)

Arguments

grl	GRangesList object
strandSpecific	logical indicating whether the gaps are calculated per strand, see `getGRLgaps()`.
gapname, suffix	character vector supplying the name to assign to new gap GRanges elements, using `jamba::makeNames()` with `suffix` as described to define non-duplicated names. If `gapname is NULL` then no names are assigned to new gap GRanges entries, however when the input `gr` GRanges object has names, the concatenation of gaps causes names `""` to be assigned to all gap GRanges elements, which are duplicated for multiple gaps.
newValues	list of values to add to the resulting gap GRanges, whose names become `colnames(grl@unlistData)`, and whose values are used to populate each column. By default a colname `"feature_type"` is added, with value `"gap"` added to each row. When `newValues` is `NULL` then no values are added to the gaps GRanges. For every entry in `names(newValues)`, if the colname does not exist, it is created and populated with `default_feature_type` as a default value, prior to adding gaps.
default_feature_type, feature_type_colname	character values, indicating the type and colname to populate in `values(grl@unlistData)` prior to adding gaps. When `feature_type_colname` is NULL, no action is taken. When `feature_type_colname` does not exist in `colnames(values(grl@unlistData))`, it is created with values in `default_feature_type`. Also any colname defined by `newValues` that does not already exist is also created and populated with `default_feature_type`.
doSort	logical indicating whether to sort the resulting GRanges objects. When `doSort=FALSE` the gaps are added to the end of each input `grl` GRanges object. Note that the GrangesList object is not sorted, only the GRanges objects within the GRangesList are sorted.
verbose	logical indicating whether to print verbose output.
...	additional arguments are passed to `getGRLgaps()`.

Value

GRangesList object, sorted per GRangesList element when doSort=TRUE. When newValues is supplied, the values for gaps GRanges elements will be assigned, otherwise any column values present in gr will be NA for gaps elements. The names of gaps elements are assigned using gapname then are made unique using jamba::makeNames(), unless gapname is NULL.

Details

This function adds gaps between each GRanges region separately for each GRangesList element, where there is a gap between two GRanges for the same seqnames. When strandSpecific=TRUE the gaps are determined per strand.

This function is a wrapper around getGRLgaps(), which is then concatenated to the input gr GRanges object using S4Vectors::pc(). When the input grl GRanges has column S4Vectors::values() then the gaps GRanges object will have NA values used by default. To supply values, use the newValues argument, which assigns name-value pairs.

Examples

gr <- GenomicRanges::GRanges(seqnames=rep(c("chr1","chr2"), c(3,2)),
   ranges=IRanges::IRanges(start=c(100, 300, 400, 300, 700),
      end=c(199, 450, 500, 600, 800)),
   strand=rep(c("+","-"), c(3,2)),
   feature_type=rep("exon", 5));
names(gr) <- jamba::makeNames(rep("exon", length(gr)));
gr;
#> GRanges object with 5 ranges and 1 metadata column:
#>           seqnames    ranges strand | feature_type
#>              <Rle> <IRanges>  <Rle> |  <character>
#>   exon_v1     chr1   100-199      + |         exon
#>   exon_v2     chr1   300-450      + |         exon
#>   exon_v3     chr1   400-500      + |         exon
#>   exon_v4     chr2   300-600      - |         exon
#>   exon_v5     chr2   700-800      - |         exon
#>   -------
#>   seqinfo: 2 sequences from an unspecified genome; no seqlengths
addGRgaps(gr);
#> GRanges object with 7 ranges and 1 metadata column:
#>           seqnames    ranges strand | feature_type
#>              <Rle> <IRanges>  <Rle> |  <character>
#>   exon_v1     chr1   100-199      + |         exon
#>    gap_v1     chr1   200-299      + |          gap
#>   exon_v2     chr1   300-450      + |         exon
#>   exon_v3     chr1   400-500      + |         exon
#>   exon_v4     chr2   300-600      - |         exon
#>    gap_v2     chr2   601-699      - |          gap
#>   exon_v5     chr2   700-800      - |         exon
#>   -------
#>   seqinfo: 2 sequences from an unspecified genome; no seqlengths

grl <- GenomicRanges::split(gr, GenomicRanges::seqnames(gr));
grl;
#> GRangesList object of length 2:
#> $chr1
#> GRanges object with 3 ranges and 1 metadata column:
#>           seqnames    ranges strand | feature_type
#>              <Rle> <IRanges>  <Rle> |  <character>
#>   exon_v1     chr1   100-199      + |         exon
#>   exon_v2     chr1   300-450      + |         exon
#>   exon_v3     chr1   400-500      + |         exon
#>   -------
#>   seqinfo: 2 sequences from an unspecified genome; no seqlengths
#> 
#> $chr2
#> GRanges object with 2 ranges and 1 metadata column:
#>           seqnames    ranges strand | feature_type
#>              <Rle> <IRanges>  <Rle> |  <character>
#>   exon_v4     chr2   300-600      - |         exon
#>   exon_v5     chr2   700-800      - |         exon
#>   -------
#>   seqinfo: 2 sequences from an unspecified genome; no seqlengths
#> 
addGRLgaps(grl);
#> GRangesList object of length 2:
#> $chr1
#> GRanges object with 4 ranges and 1 metadata column:
#>           seqnames    ranges strand | feature_type
#>              <Rle> <IRanges>  <Rle> |  <character>
#>   exon_v1     chr1   100-199      + |         exon
#>    gap_v1     chr1   200-299      + |          gap
#>   exon_v2     chr1   300-450      + |         exon
#>   exon_v3     chr1   400-500      + |         exon
#>   -------
#>   seqinfo: 2 sequences from an unspecified genome; no seqlengths
#> 
#> $chr2
#> GRanges object with 3 ranges and 1 metadata column:
#>           seqnames    ranges strand | feature_type
#>              <Rle> <IRanges>  <Rle> |  <character>
#>   exon_v4     chr2   300-600      - |         exon
#>    gap_v2     chr2   601-699      - |          gap
#>   exon_v5     chr2   700-800      - |         exon
#>   -------
#>   seqinfo: 2 sequences from an unspecified genome; no seqlengths
#> 
addGRLgaps(grl, strandSpecific=FALSE);
#> GRangesList object of length 2:
#> $chr1
#> GRanges object with 4 ranges and 1 metadata column:
#>           seqnames    ranges strand | feature_type
#>              <Rle> <IRanges>  <Rle> |  <character>
#>   exon_v1     chr1   100-199      + |         exon
#>   exon_v2     chr1   300-450      + |         exon
#>   exon_v3     chr1   400-500      + |         exon
#>    gap_v1     chr1   200-299      * |          gap
#>   -------
#>   seqinfo: 2 sequences from an unspecified genome; no seqlengths
#> 
#> $chr2
#> GRanges object with 3 ranges and 1 metadata column:
#>           seqnames    ranges strand | feature_type
#>              <Rle> <IRanges>  <Rle> |  <character>
#>   exon_v4     chr2   300-600      - |         exon
#>   exon_v5     chr2   700-800      - |         exon
#>    gap_v2     chr2   601-699      * |          gap
#>   -------
#>   seqinfo: 2 sequences from an unspecified genome; no seqlengths
#>

Add gaps between GRangesList regions

Arguments

Value

Details

See also

Examples