eveilyeverafter HMMancestry issues

eveilyeverafter / HMMancestry

R package using the Forward-Backward algorithm to infer genotypes, recombination hotspots, and gene conversion tracts from low-coverage next-generation sequence data.

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Removing the R variants of the FB algorithms

#23 eveilyeverafter closed 8 years ago
0
hill climbing function not working

#22 eveilyeverafter closed 8 years ago
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Make impute function that infers genotypes between known snps

#21 eveilyeverafter closed 8 years ago
0
update R's diploid FB algorithm with updated T matrix

#20 eveilyeverafter closed 9 years ago
0
Check en_masse simulation

#19 eveilyeverafter closed 8 years ago
0
Choice of Haldane or Kosambi mapping functions

#18 eveilyeverafter closed 9 years ago
1
Transition matrix when snp displacement is large

#17 eveilyeverafter closed 9 years ago
1
Maximum likelihood estimation for p.assign and p.trans parameters needed

#16 eveilyeverafter closed 9 years ago
4
add dependencies

#15 eveilyeverafter closed 9 years ago
0
unknown macros when roxygenizing the package

#14 eveilyeverafter closed 9 years ago
1
equations in roxygen

#13 eveilyeverafter closed 8 years ago
0
Need proper workflow for testthat

#12 eveilyeverafter closed 8 years ago
0
dplyr required for one of my examples

#11 eveilyeverafter closed 9 years ago
4
use fb algorithm for single spores or non-yeast sexually reproducing organisms.

#10 eveilyeverafter closed 9 years ago
1
simulating gene conversion

#9 eveilyeverafter closed 9 years ago
2
Error in if (CO_summary$GCbias[res_range[1] - 1] == 2 & CO_summary$GCbias[res_range[2] + : missing value where TRUE/FALSE needed

#8 eveilyeverafter closed 9 years ago
1
Error in if (sums[a] != 2) { : missing value where TRUE/FALSE needed

#7 eveilyeverafter closed 9 years ago
1
estimate_anc_fwd_back() fails when simulate_coverage() simulates high read coverage.

#6 eveilyeverafter closed 9 years ago
1
output format change request for estimate_anc_fwd_back()

#5 eveilyeverafter closed 9 years ago
1
The product of the forward and backward probabilities = 0 in some cases.

#4 eveilyeverafter closed 9 years ago
1
Viterbi algorithm when sequence coverage is low.

#3 eveilyeverafter closed 9 years ago
1
Realistic recombination

#2 eveilyeverafter closed 9 years ago
1
the FB and Viterbi algorithms input

#1 eveilyeverafter closed 9 years ago
2