integer-utils: Some utility functions to operate on integer vectors
In S4Vectors: Foundation of vector-like and list-like containers in Bioconductor

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

Some low-level utility functions to operate on ordinary integer vectors.

isSequence(x, of.length=length(x))

toListOfIntegerVectors(x, sep=",")

## more to come...

x

For isSequence(): An integer vector.

For toListOfIntegerVectors(): A character vector where each element is a string containing comma-separated integers in decimal representation. Alternatively x can be a list of raw vectors, in which case it's treated like if it was sapply(x, rawToChar).

of.length

The expected length of the integer sequence.

sep

The separator represented as a single-letter string.

isSequence() returns TRUE or FALSE depending on whether x is identical to seq_len(of.length) or not.

toListOfIntegerVectors() is a fast and memory-efficient implementation of

1	lapply(strsplit(x, sep, fixed=TRUE), as.integer)

but, unlike the above code, it will raise an error if the input contains NAs or strings that don't represent integer values.

A list parallel to x where each list element is an integer vector.

Hervé Pagès

The seq_len function in the base package.
The strsplit function in the base package.

## ---------------------------------------------------------------------
## isSequence()
## ---------------------------------------------------------------------
isSequence(1:5)               # TRUE
isSequence(5:1)               # FALSE
isSequence(0:5)               # FALSE
isSequence(integer(0))        # TRUE
isSequence(1:5, of.length=5)  # TRUE (the expected length)
isSequence(1:5, of.length=6)  # FALSE (not the expected length)

## ---------------------------------------------------------------------
## toListOfIntegerVectors()
## ---------------------------------------------------------------------

x <- c("1116,0,-19",
       " +55291 , 2476,",
       "19184,4269,5659,6470,6721,7469,14601",
       "7778889, 426900, -4833,5659,6470,6721,7096",
       "19184 , -99999")

y <- toListOfIntegerVectors(x)
y

## When it doesn't choke on an NA or string that doesn't represent
## an integer value, toListOfIntegerVectors() is equivalent to
## the function below but is faster and more memory-efficient:
toListOfIntegerVectors2 <- function(x, sep=",")
{
    lapply(strsplit(x, sep, fixed=TRUE), as.integer)
}
y2 <- toListOfIntegerVectors2(x)
stopifnot(identical(y, y2))