Views-utils {IRanges} | R Documentation |
The slice
function creates a Views object that contains
the indices where the data are within the specified bounds.
The viewMins
, viewMaxs
, viewSums
, viewMeans
functions calculate the minima, maxima, sums, and means on views respectively.
viewApply(X, FUN, ..., simplify = TRUE) slice(x, lower=-Inf, upper=Inf, ...) ## S4 method for signature 'Rle': slice(x, lower=-Inf, upper=Inf, includeLower=TRUE, includeUpper=TRUE, rangesOnly = FALSE) viewMins(x, na.rm=FALSE) viewMaxs(x, na.rm=FALSE) viewSums(x, na.rm=FALSE) viewMeans(x, na.rm=FALSE) viewWhichMins(x, na.rm=FALSE) viewWhichMaxs(x, na.rm=FALSE) viewRangeMins(x, na.rm=FALSE) viewRangeMaxs(x, na.rm=FALSE)
X |
A Views object. |
FUN |
The function to be applied to each view in X .
|
... |
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 Rle, RleList, XInteger object
or an integer vector for slice .
An RleViews, RleViewsList,
XIntegerViews object for
An Rle, RleViewsList,
XIntegerViews object for |
lower, upper |
The lower and upper bounds for the slice. |
includeLower, includeUpper |
Logical indicating whether or not the specified boundary is open or closed. |
rangesOnly |
For Rle and RleList objects, a logical indicating whether or not to drop the original data from the output. |
na.rm |
Logical indicating whether or not to include missing values in the results. |
The slice
function is useful for finding areas of absolute maxima
(peaks), absolute minima (troughs), or fluctuations within specified limits.
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.
An RleViews object for Rle or an
RleViewsList for RleList containing the
views when using slice
with rangesOnly = FALSE
.
An IRanges object for Rle or a
CompressedIRangesList for RleList containing
the ranges when using slice
with rangesOnly = TRUE
.
An XIntegerViews for an XInteger object
when using slice
.
A vector of length(x)
for RleViews and
XIntegerViews objects or a SimpleList object of
length(x)
for RleViewsList objects containing the
numeric summaries for the views for viewMins
, viewMaxs
,
viewSums
, viewMeans
, viewWhichMins
, and
viewWhichMaxs
.
An IRanges object for RleViews objects or a
SimpleIRangesList for RleViewsList objects
containing the location ranges for viewRangeMins
and
viewRangeMaxs
.
P. Aboyoun
RleViews-class, RleViewsList-class, XIntegerViews-class,
which.min
, colSums
## Views derived from vector vec <- as.integer(c(19, 5, 0, 8, 5)) slice(vec, lower=5, upper=8) set.seed(0) vec <- sample(24) vecViews <- slice(vec, lower=4, upper=16) vecViews viewApply(vecViews, function(x) diff(as.integer(x))) viewMins(vecViews) viewMaxs(vecViews) viewSums(vecViews) viewMeans(vecViews) viewWhichMins(vecViews) viewWhichMaxs(vecViews) ## Views derived from coverage x <- IRanges(start=c(1L, 9L, 4L, 1L, 5L, 10L), width=c(5L, 6L, 3L, 4L, 3L, 3L)) slice(coverage(x), lower=2) slice(coverage(x), lower=2, rangesOnly = TRUE)