mdavy86/polymapr

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polymapr's Issues

Genotype conversion into missing data for one of the 2 parents

Hi,

I am testing poolymapR for a set of markers that were used to genotype a population of an autotetraploid species. When I run the checkF1 function, one of my parents is converted into missing (NA) and I do not understand why. Below is an example of the file for reproducing the error.

test_finalUpdog.txt

This is the code that I am using:

tmp2 <- read.delim('test_finalUpdog.tab', header = TRUE, sep = '\t', row.names = 1)

tmp <- as.matrix(tmp2)

bF1checked <- checkF1(dosage_matrix = tmp2, parent1 = "RM55_R1", parent2 = "RM59_R1", F1 = colnames(tmp2)[3:ncol(tmp2)], polysomic = TRUE, disomic = FALSE, mixed = FALSE, ploidy = 4)

head(bF1checked)

Any help will be appreciated!

Kostas