subset,GenoGAMList-method {GenoGAM} | R Documentation

## Subset method for GenoGAMList

### Description

Subset method for GenoGAMList

### Usage

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

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

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

### Arguments

`x` | A GenoGAMList 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.

### Details

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

### Value

A subsetted GenoGAMList object.

### Author(s)

Georg Stricker georg.stricker@in.tum.de

### References

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

[Package GenoGAM version 2.10.0 Index]