This program takes a matrix and orders
the content of each cell. It was specially designed
for genetic data, but can be used with any data
that can be rearranged by the function order.
The arguments ploidy and ncode determine the mode of
ordering the data.
The cells corresponding to each individual i and
loci j are ordered in ascending order in default option
(it can be passed decreasing = TRUE as argument, if descending order is desired).
For example, a locus with ploidy = 2 and ncod =1, coded as 51,
for an individual, will be recoded as 15. A locus with ploidy = 3
and coded as 143645453, will be recoded as 143453645 (alleles 143, 454 and 645).
aue.sort(X, ncod = NULL, ploidy = 2, sep.loc = "", chk.plocod = TRUE, ...)
| X | Any matrix with content to order. |
|---|---|
| ncod | Number of digits coding each allele (e.g., 1: x, 2: xx, 3: xxx, etc.). If NULL, ncode will we obtained from the ploidy and the maximum number of characters in the data cells. |
| ploidy | Ploidy of the data. |
| sep.loc | Character string separating alleles. |
| chk.plocod | Defalult TRUE. The function checks coherence in ploidy and number of digits coding alleles. |
| ... | Additional arguments passed to |
# NOT RUN { # Example 1---------------------- geno <- c(12, 52, 62, 45, 54, 21) geno <- matrix(geno, 3, 2) # ordering the data aue.sort(geno, ploidy = 2) # decreasing sort order aue.sort(geno, ploidy = 2, decreasing = TRUE) # Example 2---------------------- geno2 <- c(123456, 524556, 629359, 459459, 543950, 219405) geno2 <- matrix(geno2, 3, 2) # ordering the data as diploid aue.sort(geno2, ploidy = 2) # the data is ordered using blocks of 3 characters # ordering the data as triploid aue.sort(geno2, ploidy = 3) # the data is ordered using blocks of 2 characters # error: the ploidy and the number of characters are not congruent aue.sort(geno2, ploidy = 5) # error: the ploidy and the number of characters are not congruent aue.sort(geno2, ploidy = 5) # Example 3---------------------- # any character data generic <- c("aldk", "kdbf", "ndnd", "ndkd") generic <- matrix(generic, 2, 2) aue.sort(generic, ploidy = 2) aue.sort(generic, ploidy = 4) # }