IRanges (version 2.6.1)

AtomicList-utils: Common operations on AtomicList objects

Description

Common operations on AtomicList objects.

Group Generics

AtomicList objects have support for S4 group generic functionality to operate within elements across objects:

Arith

"+", "-", "*", "^", "%%", "%/%", "/"

Compare

"==", ">", "<"< code="">, "!=", "<="< code="">, ">="

Logic

"&", "|"

Ops

"Arith", "Compare", "Logic"

Math

"abs", "sign", "sqrt", "ceiling", "floor", "trunc", "cummax", "cummin", "cumprod", "cumsum", "log", "log10", "log2", "log1p", "acos", "acosh", "asin", "asinh", "atan", "atanh", "exp", "expm1", "cos", "cosh", "sin", "sinh", "tan", "tanh", "gamma", "lgamma", "digamma", "trigamma"

Math2

"round", "signif"

Summary

"max", "min", "range", "prod", "sum", "any", "all"

Complex

"Arg", "Conj", "Im", "Mod", "Re"

See S4groupGeneric for more details.

Other Methods

The AtomicList objects also support a large number of basic methods. Like the group generics above, these methods perform the corresponding operation on each element of the list separately. The methods are:

Logical

!, which, which.max, which.min

Numeric

diff, pmax, pmax.int, pmin, pmin.int, mean, var, cov, cor, sd, median, quantile, mad, IQR

Running Window

smoothEnds, runmed. runmean, runsum, runwtsum, runq

Character

nchar, chartr, tolower, toupper, sub, gsub

Specialized Methods

unstrsplit(x, sep="")

: A fast sapply(x, paste0, collapse=sep). See ?unstrsplit for the details.

See Also

• AtomicList objects.

Examples

## group generics
int1 <- c(1L,2L,3L,5L,2L,8L)
int2 <- c(15L,45L,20L,1L,15L,100L,80L,5L)
col1 <- IntegerList(one = int1, int2)
2 * col1
col1 + col1
col1 > 2
sum(col1)  # equivalent to (but faster than) 'sapply(col1, sum)'
mean(col1)  # equivalent to 'sapply(col1, mean)'