Hello All,
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I am trying to use LINKMFEX to check (and, if possible, correct) Mendelian Inheritance errors in a dataset to be used for linkage mapping.
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I am struggling to get consistent information from the LINKMFEX manual, and I could use some directions from anyone that used this software before.
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The only information the manual gives is:
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- "LepMap formatted genotype files"
- "comma delimited or .csv file"
- "the first two rows must be the parents of the family"
- "the first line . . .No_of_loci, X" where X is the number of loci
- "the second line. . .No_of_progeny, Y" Y is number of offspring
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Using that information, I produced a file similar to the one below
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No_of_loci,3
No_of_progeny,3
1,1,0,0,1,0,1,2,1,1,1,2
1,2,0,0,2,0,1,2,1,2,0,0
1,3,1,2,0,0,1,1,1,1,1,1
1,4,1,2,0,0,1,2,1,2,1,2
1,5,1,2,0,0,2,2,1,2,1,2
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each row is an individual, the first 6 columns are pedigree data (LepMap format, linkage format) and the remaining columns are alleles (2 alleles per locus).
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The first row then states:
Family, IndividualID, FatherID, MotherID,Sex,Phenotype, Locus1-allele1, Locus1-allele2, etc
1, 1, 0,0,1,0,1,2,1,1,1,2
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Family = 1, ID = 1, father = 0 = unknown, mother = 0 = unknown, sex= 1 = male, phenotype = 0 = unknown, locus 1 = 12 = heterozygote, locu 2 = 11 = homozygote, etc
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I checked that no spaces are present, but when I select the file I get the message:
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"Run-time error '9':
Subscript out of range"
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Any help is greatly appreciated as documentation for this software is limited.
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Kind regards,
Lorenzo
Dear ResearchGate community,
After a good night of sleep I was able to understand the issue. Being that each file contains one family, and that parents for the whole file are the first two rows of data, I realized that the first 6 columns are superfluous and resulted in the "subscript out of bounds error"
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Thus, the corrected file looks like this:
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No_of_loci,3
No_of_progeny,3
1,2,1,1,1,2
1,2,1,2,0,0
1,1,1,1,1,1
1,2,1,2,1,2
2,2,1,2,1,2
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