AtomicList-utils: Common operations on AtomicList objects
In IRanges: Foundation of integer range manipulation in Bioconductor

Description Group Generics Other Methods Specialized Methods Author(s) See Also Examples

Common operations on AtomicList objects.

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

Arith: "+", "-", "*", "^", "%%", "%/%", "/"
Compare: "==", ">", "<", "!=", "<=", ">="
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.

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

The which.min and which.max functions have an extra argument, global=FALSE, which controls whether the returned subscripts are global (compatible with the unlisted form of the input) or local (compatible with the corresponding list element).

The rank method only supports tie methods “average”, “first”, “min” and “max”.

Since ifelse relies on non-standard evaluation for arguments that need to be in the generic signature, we provide ifelse2, which has eager but otherwise equivalent semantics.

: unstrsplit(x, sep="")

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

P. Aboyoun

AtomicList objects.

## 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)'