Question: ASMap for the qtl/r data
0
gravatar for mad.cichlids
2 days ago by
mad.cichlids120
Texas
mad.cichlids120 wrote:

Hi, I am trying to build a genetic map with "ASMap" package using the F2 intercross data. The dataformat was initially prepared for qtl package.And the data in the qtl/r package works just fine, but it produces an error in "ASMap". And I did use the convert2bcsft() function to convert it to the format that the ASMap suppose to understand. Anyone has come across the same problem?

Here is the detail:

mapthis = read.cross("csv", "", "mydata.csv", na.strings="NA", genotypes=c("PP","CP","CC"), alleles=c("P","C"), estimate.map=FALSE)

--Read the following data: 251 individuals 7053 markers 29 phenotypes --Cross type: f2 Warning message: In summary.cross(cross) : Some chromosomes > 1000 cM in length; there may be a problem with the genetic map. (Perhaps it is in basepairs?)

mapthis <- convert2bcsft(mapthis, BC.gen=0, F.gen=2, estimate.map=FALSE)

summary(mapthis)

BC(0)F(2) cross

No. individuals:    251 

No. phenotypes:     29 
Percent phenotyped: 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 
                    100 100 99.2 99.2 99.6 99.6 99.6 100 99.6 99.6 100 99.6 99.6 

No. chromosomes:    8 
    Autosomes:      1 2 3 4 5 6 7 8 

Total markers:      7053 
No. markers:        730 978 829 700 771 1153 984 908 
Percent genotyped:  88.1 
Genotypes (%):      PP:20.7  PC:46.1  CC:33.2  not CC:0.0  not PP:0.0

Warning message: In summary.cross(mapthis) : Some chromosomes > 1000 cM in length; there may be a problem with the genetic map. (Perhaps it is in basepairs?)

sg <- statGen(mapthis, bychr = FALSE, stat.type = "miss")

Error in statGen(mapthis, bychr = FALSE, stat.type = "miss") : The unique identifier for the genotypes, "Genotype", cannot be found in the object

ADD COMMENTlink modified 1 day ago • written 2 days ago by mad.cichlids120
0
gravatar for julian.taylor
1 day ago by
julian.taylor0 wrote:

Check ?statGen .. you need the correct column name of mapthis$pheno to be passed to the "id" argument of statGen().

ADD COMMENTlink written 1 day ago by julian.taylor0

Can you please elaborate this? When I check the mapthis$pheno, it is a matrix of all phenotype data. This is the part that is puzzling me, what would a "correct column" name to pass the id argument (which requires genotype information? Thanks!

ADD REPLYlink written 1 day ago by mad.cichlids120
0
gravatar for mad.cichlids
1 day ago by
mad.cichlids120
Texas
mad.cichlids120 wrote:

okay, finally figured it out. I checked the example file in the ASMap. the data is really just individual id with the genotype information. However, in the qtl data format, it usually consists of phenotype and genotype and indivudual id, when I pass the individual id information to the "id" argument, it works! Thanks again!

ADD COMMENTlink written 1 day ago by mad.cichlids120
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