Description Usage Arguments Details Value Author(s) References Examples

Subset methods for GenoGAMDataSet

1 2 3 4 5 6 7 8 9 10 | ```
## 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 The |

`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

1 2 3 4 5 6 7 8 9 10 11 12 | ```
# 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)
``` |

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