ASMap for the qtl/r data
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4 months ago
mad.cichlids ▴ 120

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

R marker odering genetic map ASMap linkage group • 339 views
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Entering edit mode
4 months ago

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

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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!

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4 months ago
mad.cichlids ▴ 120

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!

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I am having the exact same issue working with f2 gbs data in R/qtl to ASMap importing. After converting convert2bcsft(), when I run sg <- statGen(mapthis, bychr = FALSE, stat.type = "miss"), it gave the exact same error msg you mentioned. Input data in csv were arranged according to R/qtl format. I would be thankful if got to know the trick or idea to overcome this issue. Thanks!

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you need to add "id" argument. In rqtl, the first column can be either phenotype, or identifier for the individuals, if you pass the individual id column to the "id" argument, it will work, least to me.

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