# GenoGAMList-subsetting: Subset method for GenoGAMList In GenoGAM: A GAM based framework for analysis of ChIP-Seq data

## Description

Subset method for GenoGAMList

## Usage

 ``` 1 2 3 4 5 6 7 8 9 10``` ```## 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 [email protected]

## 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

GenoGAM documentation built on Dec. 7, 2018, 6 p.m.