mixedSort {jamba}R Documentation

sort alphanumeric values keeping numeric values in proper order

Description

sort alphanumeric values keeping numeric values in proper order

Usage

mixedSort(
  x,
  blanksFirst = TRUE,
  na.last = NAlast,
  keepNegative = FALSE,
  keepInfinite = FALSE,
  keepDecimal = FALSE,
  ignore.case = TRUE,
  useCaseTiebreak = TRUE,
  honorFactor = FALSE,
  sortByName = FALSE,
  verbose = FALSE,
  NAlast = TRUE,
  ...
)

Arguments

x

vector

blanksFirst

logical whether to order blank entries before entries containing a value.

na.last

logical indicating whether to move NA entries at the end of the sort.

keepNegative

logical whether to keep '-' associated with adjacent numeric values, in order to sort them as negative values.

keepInfinite

logical whether to allow "Inf" to be considered a numeric infinite value.

keepDecimal

logical whether to keep the decimal in numbers, sorting as a true number and not as a version number. By default keepDecimal=FALSE, which means "v1.200" should be ordered before "v1.30". When keepDecimal=TRUE, the numeric sort considers only "1.2" and "1.3" and sorts in that order.

ignore.case

logical whether to ignore uppercase and lowercase characters when defining the sort order. Note that when x is factor the factor levels are converted using unique(toupper(levels(x))), therefore the values in x will be sorted by factor level.

useCaseTiebreak

logical indicating whether to break ties when ignore.case=TRUE, using mixed case as a tiebreaker.

honorFactor

logical, default TRUE, indicating whether to honor factor level order in the output, otherwise when FALSE it sorts as character.

sortByName

logical whether to sort the vector x by names(x) instead of sorting by x itself.

verbose

logical whether to print verbose output.

NAlast

logical deprecated in favor of argument na.last for consistency with base::sort().

...

additional parameters are sent to mixedOrder.

Details

This function is a refactor of gtools mixedsort(), a clever bit of R coding from the gtools package. It was extended to make it slightly faster, and to handle special cases slightly differently. It was driven by the need to sort gene symbols, miRNA symbols, chromosome names, all with proper numeric order, for example:

test set:

miR-12,miR-1,miR-122,miR-1b,mir-1a

gtools::mixedsort:

miR-122,miR-12,miR-1,miR-1a,mir-1b

mixedSort:

miR-1,miR-1a,miR-1b,miR-12,miR-122

The function does not by default recognize negative numbers as negative, instead it treats '-' as a delimiter, unless keepNegative=TRUE.

This function also attempts to maintain '.' as part of a decimal number, which can be problematic when sorting IP addresses, for example.

This function is really just a wrapper function for mixedOrder(), which does the work of defining the appropriate order.

The sort logic is roughly as follows:

Therefore, some expected behaviors:

Value

vector of values from argument x, ordered by mixedOrder(). The output class should match class(x).

See Also

Other jam sort functions: mixedOrder(), mixedSortDF(), mixedSorts(), mmixedOrder()

Examples

x <- c("miR-12","miR-1","miR-122","miR-1b", "miR-1a", "miR-2");
sort(x);
mixedSort(x);

# test honorFactor
mixedSort(factor(c("Cnot9", "Cnot8", "Cnot10")))
mixedSort(factor(c("Cnot9", "Cnot8", "Cnot10")), honorFactor=TRUE)

# test ignore.case
mixedSort(factor(c("Cnot9", "Cnot8", "CNOT9", "Cnot10")))
mixedSort(factor(c("CNOT9", "Cnot8", "Cnot9", "Cnot10")))
mixedSort(factor(c("Cnot9", "Cnot8", "CNOT9", "Cnot10")), ignore.case=FALSE)
mixedSort(factor(c("Cnot9", "Cnot8", "CNOT9", "Cnot10")), ignore.case=TRUE)

mixedSort(factor(c("Cnot9", "Cnot8", "CNOT9", "Cnot10")), useCaseTiebreak=TRUE)
mixedSort(factor(c("CNOT9", "Cnot8", "Cnot9", "Cnot10")), useCaseTiebreak=FALSE)


[Package jamba version 1.0.4 Index]