Class | Analysis and data manipulation command |
Name | recode |
Arguments | (<marker>|$(m|x)) [frequencies | letter | number] |
Recodes alleles at that marker or set of markers to 1..N, where the ordering defaults to the allele size (or collation order for letter alleles). If the freq modifier is present, the numbering is by ascending allele frequency. If the let modifier is present, the numbering is "1..4" for "ACGT", and the reverse for num.
Example:
>> wri 1 1 x x x A/C 2 2 x x x C/C 3 3 x x x A/A 4 4 x x x A/A >> recode $m num Recoding nucleotide letter alleles to number code (ACGT->1234). >> wri 1 1 x x x 1/2 2 2 x x x 2/2 3 3 x x x 1/1 4 4 x x x 1/1 >> recode $m let Recoding numbered alleles to nucleotide letter code (1234->ACGT). >> recode $m fre Renumbering alleles at "m" to 1.. 2. Ordering by sample allele frequency. >> wri 1 1 x x x 1/2 2 2 x x x 1/1 3 3 x x x 2/2 4 4 x x x 2/2
Class | Analysis and data manipulation command |
Name | recode |
Arguments | <marker> <all1|value1>...<allN|valueN> to <new allele|new value> [...<newN>].. |
Allows pooling and/or recoding of marker alleles prior to subsequent analysis. If there are fewer new values than old values, the last new value is recycled.
Example:
>> recode marker1 1 2 to A C Recoding locus marker1 From: 1 2 To : A C Recoded 16 values. >> recode marker2 100 102 104 to 99 Recoding locus marker2 From: 100 102 104 To : 99
<< (get) | Up to index | >> (combine) |