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) ## 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 Rle, RleList, XInteger object
or an integer vector for An RleViews, RleViewsList,
XIntegerViews or XDoubleViews object
for An Rle, RleViewsList,
XIntegerViews or XDoubleViews 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.
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).
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
.
An XDoubleViews for an XDouble object
when using slice
.
A vector of length(x)
for RleViews,
XIntegerViews and XDoubleViews 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)