gravatar for mad.cichlids

2 hours ago by

Texas

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

link

modified 1 hour ago

written
2 hours ago
by

mad.cichlids120



Source link