GenoGAMDataSet-subsetting: Subset methods for GenoGAMDataSet
In gstricker/GenoGAM: A GAM based framework for analysis of ChIP-Seq data

Description Usage Arguments Details Value Author(s) References Examples

Subset methods for GenoGAMDataSet

## S4 method for signature 'GenoGAMDataSet'
subset(x, ...)

## S4 method for signature 'GenoGAMDataSet,GRanges'
subsetByOverlaps(x, ranges,
  maxgap = -1L, minoverlap = 0L, type = c("any", "start", "end",
  "within", "equal"), invert = FALSE, ...)

## S4 method for signature 'GenoGAMDataSet,GRanges,ANY,ANY'
x[i]

`x`	A GenoGAMDataSet object.
`...`	Further arguments. Mostly a logical statement in case of the 'subset' function. Note that the columnnames for chromosomes and positions are: 'seqnames' and 'pos'.
`ranges, i`	A GRanges object. In case of subsetting by double brackets 'i' is the index of the tile.
`maxgap, minoverlap`	Intervals with a separation of 'maxgap' or less and a minimum of 'minoverlap' overlapping positions, allowing for 'maxgap', are considered to be overlapping. 'maxgap' should be a scalar, non-negative, integer. 'minoverlap' should be a scalar, positive integer.
`type`	By default, any overlap is accepted. By specifying the 'type' parameter, one can select for specific types of overlap. The types correspond to operations in Allen's Interval Algebra (see references in). If `type` is `start` or `end`, the intervals are required to have matching starts or ends, respectively. While this operation seems trivial, the naive implementation using `outer` would be much less efficient. Specifying `equal` as the type returns the intersection of the `start` and `end` matches. If `type` is `within`, the query interval must be wholly contained within the subject interval. Note that all matches must additionally satisfy the `minoverlap` constraint described above. The `maxgap` parameter has special meaning with the special overlap types. For `start`, `end`, and `equal`, it specifies the maximum difference in the starts, ends or both, respectively. For `within`, it is the maximum amount by which the query may be wider than the subject.
`invert`	If TRUE, keep only the query ranges that do _not_ overlap the subject.

Those are various methods to subset the GenoGAMDataSet object. By logical statement or GRanges overlap. The '[' subsetter is just a short version of 'subsetByOverlaps'.

A subsetted GenoGAMDataSet object.

Georg Stricker georg.stricker@in.tum.de

Allen's Interval Algebra: James F. Allen: Maintaining knowledge about temporal intervals. In: Communications of the ACM. 26/11/1983. ACM Press. S. 832-843, ISSN 0001-0782

# subset by overlaps
ggd <- makeTestGenoGAMDataSet()
SummarizedExperiment::rowRanges(ggd)
gr <- GenomicRanges::GRanges("chrI", IRanges(10000,19000))
res <- IRanges::subsetByOverlaps(ggd, gr)
SummarizedExperiment::rowRanges(res)

# Subset by logical statement
ggd <- makeTestGenoGAMDataSet()
SummarizedExperiment::rowRanges(ggd)
res <- subset(ggd, seqnames == "chrI" & pos <= 17000)
SummarizedExperiment::rowRanges(res)