Sib-pair Command: recode


ClassAnalysis and data manipulation command
Namerecode
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


Sib-pair Command: recode


ClassAnalysis and data manipulation command
Namerecode
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

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