This function interconverts genetic data among matrix format (one locus or one allele per column) and list format (one locus or one allele per column).
eco.convert(X, input = c("matrix", "alleles.matrix", "list", "alleles.list"), output = c("matrix", "alleles.matrix", "list", "alleles.list"), ncod = NULL, ploidy = 2, sep.in, sep.out, chk.names = TRUE, chk.plocod = TRUE)
| X | Input data. |
|---|---|
| input | Input data format. |
| output | Output data format. |
| ncod | Number of digits coding each allele. |
| ploidy | Ploidy of the data. |
| sep.in | Character separating alleles in the input data if present. |
| sep.out | Character separating alleles in the output data. Default option do not separate alleles. |
| chk.names | Defalult TRUE. The function makes checks of individuals and loci names during conversion. |
| chk.plocod | Defalult TRUE. The function checks coherence in/between ploidy and number of digits coding alleles for loci data during conversion. |
# NOT RUN { data(eco3) # One allele per column loc2al <- eco.convert(eco3[["G"]], "matrix", "alleles.matrix", ploidy = 2) loc2al # Inverse operation (collapse alleles into locus) al2loc <- eco.convert(loc2al, "alleles.matrix", "matrix", ploidy = 2) al2loc # Separating alleles with a character string loc2loc <- eco.convert(eco3[["G"]], "matrix", "matrix", ploidy = 2, sep.out = "/") loc2loc # Inverse operation (removing separator) loc2loc.nosep <- eco.convert(loc2loc, "matrix", "matrix", ploidy = 2, sep.in = "/", sep.out = "") loc2loc.nosep # Locus to list loc2list <- eco.convert(eco3[["G"]], "matrix", "list", ploidy = 2) loc2list # Locus to allele list al2list <- eco.convert(eco3[["G"]], "matrix", "alleles.list", ploidy = 2) al2list # The inverse operations are also defined. All the formats are interconvertible. # Locus operations have defined a within operation (matrix to matrix, list to list), # with the purpose of put/remove separators between alleles. The program accepts any ploidy level. # }