Hi everyone,
I have an issue with the reshape package. Since it's quite a while that I
used it, I feel kind of rusty...
I got a data.frame like this
>
>> id Sample.Name Marker Allele.1
>> Allele.2 sample_id species
>> 1 01_primer01 Dalb01 165
>> 179 SH233 D. madagascariensis
>> 2 01_primer04 Dalb04 221
>> 225 SH233 D. madagascariensis
>> 3 01_primer08 Dalb08 218
>> 218 SH233 D. madagascariensis
>> 4 01_primer10 Dalb10 134
>> 134 SH233 D. madagascariensis
>> 5 01_primer14 Dalb14 250
>> 250 SH233 D. madagascariensis
>> 6 01_primer16 Dalb16 232
>> 232 SH233 D. madagascariensis
>>
>> this was just the head(), in fact, the sample_id col has different ids, I
>> would like to aggregate them into one
>> and I would like to get something like this:
>>
>> species sample_id Marker1_Allele1
>> Marker1_Allele2 Marker2_Allele1 Marker2_Allele2
>> (etc. 35 markers)
>>
>> D. madagascariensis SH233 179
>> 225 134
>> 244 ......
>>
>
I tried to prepare the cast() but didn't quite figure out how to achieve
this. I tried to first merge with the following:
genMelt <- melt(geno, id = c(1:2, 5:6))
then I created a column:
genMelt$Locus <- substring(as.character(genMelt$Panel),5, 6)
genMelt$Locus <- paste(genMelt$Locus, genMelt$variable, sep
= "_")
So I get a column in the appropriate format. But when I cast :
go <- cast(genMelt,sample_id~Locus)
I get just the frequencies of the Loci per sample_id
Maybe I don't even need reshape. If you have any idea on this, I appreciate
it
Cheers,
Martin
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