mstmap() error: "Non-allowable allele encodings in DH marker set" even when data format follows ASMap requirements

[huihuitaicai]

I'm using the ASMap package to construct a linkage map for a doubled haploid (DH) maize population with the mstmap() function.

I have formatted my genotype data strictly according to the requirements described in the ASMap documentation:

• Only "A" and "B" alleles are used (with U for missing data)
• All columns are of class character, not factors
• Marker names are in rownames(), individuals are in columns
• No spaces in row or column names
• No underscores in names (I've replaced them with hyphens)

Here is the code I'm running:

library(bigsnpr)
library(ASMap)
plink_prefix <- "C2_ImputationTarget_1K"
snp_readBed(paste0(plink_prefix, ".bed"))
obj.bigSNP <- snp_attach(paste0(plink_prefix, ".rds"))

G <- obj.bigSNP$genotypes[]
map_bed <- obj.bigSNP$map    

ids <- obj.bigSNP$fam$sample.ID
geno_char <- matrix(NA, nrow = nrow(G), ncol = ncol(G))
table(unlist(geno_char))
geno_char[G == 0] <- "A"
geno_char[G == 2] <- "B"
geno_char[G == 1] <- "U"
colnames(geno_char) <- obj.bigSNP$map$marker.ID
rownames(geno_char) <- obj.bigSNP$fam$sample.ID

geno_df <- as.data.frame(t(geno_char),stringsAsFactors = FALSE)
rownames(geno_df) <- gsub("_","-",rownames(geno_df))
map_list <- mstmap(geno_df, 
                   dist.fun = "kosambi",
                   trace = TRUE)

And I get the following error:

Error in mstmap.data.frame(geno_df, dist.fun = "kosambi", trace = FALSE):
  Non-allowable allele encodings in DH marker set

To troubleshoot, I’ve verified the following:

str(geno_df)
# Check allele counts
table(unlist(geno_df))
# Ensure all columns are characters
all(sapply(geno_df, is.character))  # returns TRUE
# Check for spaces in column and row names
any(grepl(" ", colnames(geno_df)))  # FALSE
any(grepl(" ", rownames(geno_df)))  # FALSE

My question

Despite confirming that my data follows the expected format for mstmap() with pop.type = "DH", I still encounter the error about non-allowable allele encodings.

Is there something I might be missing or a way to debug this further?

Thank you in advance!

[huihuitaicai]

查看原始代码中找到这一行alleles <- unique(unlist(lapply(object, unique)))，测试自己的数据，发现有NA 值，这个是不被允许的，使用geno_df[is.na(geno_df)] <- "U"之后就可以解决