genoprob_to_alleleprob return NULL in riself4

[kbroman]

It was reported at the R/qtl2 discussion group that genoprob_to_alleleprob() returned an empty list for cross type "riself4".

[kbroman]

It seems to work fine. Here's an example:

# load CC data
library(qtl2)
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/master/CC/cc.zip")
cc <- read_cross2(file)

# subset to chr 17-19
cc <- cc[,17:19]

# convert to 4-way RIL by selfing, by subsetting the founders
cc$crosstype <- "riself4"
for(i in seq_along(cc$founder_geno)) cc$founder_geno[[i]] <- cc$founder_geno[[i]][1:4,]
cc$alleles <- cc$alleles[1:4]
cc$cross_info <- t(apply(cc$cross_info, 1, function(a) a[a <= 4]))

# calculate genotype probabilities and allele probabilities
pr <- calc_genoprob(cc, cores=0)
apr <- genoprob_to_alleleprob(pr, cores=0)     

# check that there the same except for an attribute + column names
attr(apr, "alleleprobs") <- FALSE
for(i in seq_along(apr)) colnames(apr[[i]]) <- colnames(pr[[i]])
testthat::expect_equal(apr, pr)