Description Usage Arguments Details Value Note Author(s) See Also Examples

`viewApply`

applies a function on each view of a Views or
ViewsList object.

`viewMins`

, `viewMaxs`

, `viewSums`

, `viewMeans`

calculate respectively the minima, maxima, sums, and means of the views
in a Views or ViewsList object.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | ```
viewApply(X, FUN, ..., simplify = TRUE)
viewMins(x, na.rm=FALSE)
## S4 method for signature 'Views'
min(x, ..., na.rm = FALSE)
viewMaxs(x, na.rm=FALSE)
## S4 method for signature 'Views'
max(x, ..., na.rm = FALSE)
viewSums(x, na.rm=FALSE)
## S4 method for signature 'Views'
sum(x, ..., na.rm = FALSE)
viewMeans(x, na.rm=FALSE)
## S4 method for signature 'Views'
mean(x, ...)
viewWhichMins(x, na.rm=FALSE)
## S4 method for signature 'Views'
which.min(x)
viewWhichMaxs(x, na.rm=FALSE)
## S4 method for signature 'Views'
which.max(x)
viewRangeMins(x, na.rm=FALSE)
viewRangeMaxs(x, na.rm=FALSE)
``` |

`X` |
A Views object. |

`FUN` |
The function to be applied to each view in |

`...` |
Additional arguments to be passed on. |

`simplify` |
A logical value specifying whether or not the result should be simplified to a vector or matrix if possible. |

`x` |
An RleViews or RleViewsList object. |

`na.rm` |
Logical indicating whether or not to include missing values in the results. |

The `viewMins`

, `viewMaxs`

, `viewSums`

, and `viewMeans`

functions provide efficient methods for calculating the specified numeric
summary by performing the looping in compiled code.

The `viewWhichMins`

, `viewWhichMaxs`

, `viewRangeMins`

, and
`viewRangeMaxs`

functions provide efficient methods for finding the
locations of the minima and maxima.

For all the functions in this man page (except `viewRangeMins`

and
`viewRangeMaxs`

): A numeric vector of the length of `x`

if `x`

is an RleViews object, or a List object of
the length of `x`

if it's an RleViewsList object.

For `viewRangeMins`

and `viewRangeMaxs`

: An IRanges
object if `x`

is an RleViews object, or an IRangesList
object if it's an RleViewsList object.

For convenience, methods for `min`

, `max`

, `sum`

,
`mean`

, `which.min`

and `which.max`

are provided as
wrappers around the corresponding `view*`

functions (which might
be deprecated at some point).

P. Aboyoun

The

`slice`

function for slicing an Rle or RleList object.-
view-summarization-methods in the XVector package for more view summarization methods.

The RleViews and RleViewsList classes.

The

`which.min`

and`colSums`

functions.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ```
## Views derived from coverage
x <- IRanges(start=c(1L, 9L, 4L, 1L, 5L, 10L),
width=c(5L, 6L, 3L, 4L, 3L, 3L))
cvg <- coverage(x)
cvg_views <- slice(cvg, lower=2)
viewApply(cvg_views, diff)
viewMins(cvg_views)
viewMaxs(cvg_views)
viewSums(cvg_views)
viewMeans(cvg_views)
viewWhichMins(cvg_views)
viewWhichMaxs(cvg_views)
viewRangeMins(cvg_views)
viewRangeMaxs(cvg_views)
``` |

IRanges documentation built on Dec. 14, 2020, 2 a.m.

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