Some updates #27
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Some updates #27
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Updating from mmollina
update DESCRIPTION
Updating from mmollina
Example rules:
unwrapped: examples that run in < 4s
\dontrun{}: just for missing software, APIs, etc
\donttest{}: examples that take more than 4s
Functions:
- get_genomic_order: unwrapped (takes less than 1s)
- sim_homologous: (already unwrapped)
- extract_map: unwrapped (takes less than 1s)
- print_mrk: unwrapped (takes less than 1s)
- rev_map: unwrapped (takes less than 1s)
- export_map_list: unwrapped (takes less than 1s); also changed example to avoid writing local files
- drop_marker: unwrapped (takes less than 1s)
- plot_genome_vs_map: unwrapped (takes less than 1s)
- elim_redundant: (already unwrapped)
- summary_maps: removed dontrun and formattable (is not a dependency)
- segreg_poly: (already unwrapped - runs in less than 2s)
- plot_map_list: changed from dontrun to donttest (takes more than 5s)
- import_data_from_polymapR: changed from dontrun to donttest (polymapR is a suggested package)
- filter_segregation: removed dontrun because it takes less than 1s
- ls_linkage_phases: removed dontrun because it takes less than 3s
- calc_genoprob_error: changed from dontrun to donttest
- import_from_updog: changed from dontrun to donttest (updog is a suggested package)
- update_map: removed dontrun and formattable (is not a dependency)
- plot_mrk_info: removed dontrun (runs in less than 3s)
- poly_cross_simulate: (already unwrapped - runs ins less than 1s)
- read_geno_csv: changed from dontrun to donttest
- check_data_sanity: changed from dontrun to donttest
- add_marker: changed from dontrun to donttest
- make_mat_mappoly: changed from dontrun to donttest
- loglike_hmm: changed from dontrun to donttest
- dist_prob_to_class: changed from dontrun to donttest
- dist_prob_to_class: (duplicated)
- import_phased_maplist_from_polymapR: changed from dontrun to donttest (polymapR is a suggested package)
- dist_prob_to_class: (duplicated)
- update_missing: changed from dontrun to donttest
- cache_counts_twopt: changed from dontrun to donttest (also changed n.cores example from 8 to 1 due to problems when checking with --run-donttest)
- read_geno: changed from dontrun to donttest
- calc_genoprob: changed from dontrun to donttest
- export_data_to_polymapR: changed from dontrun to donttest (polymapR is a suggested package)
- get_submap: changed from dontrun to donttest
- est_rf_hmm: changed from dontrun to donttest
- mds_mappoly: changed from dontrun to donttest
- split_and_rephase: changed from dontrun to donttest
- est_rf_hmm_single: changed from dontrun to donttest
- merge_datasets: changed from dontrun to donttest
- calc_genoprob_dist: changed from dontrun to donttest
- read_geno_prob: changed from dontrun to donttest
- calc_prefpair_profiles: changed from dontrun to donttest
- est_rf_hmm_sequential: changed from dontrun to donttest
- merge_maps: changed from dontrun to donttest
- est_full_hmm_with_global_error: changed from dontrun to donttest
- calc_homoprob: changed from dontrun to donttest
- make_pairs_mappoly: changed from dontrun to donttest
- rf_list_to_matrix: changed from dontrun to donttest
- group_mappoly: changed from dontrun to donttest
- est_full_hmm_with_prior_prob: changed from dontrun to donttest
- read_vcf: changed from dontrun to donttest
- est_pairwise_rf: changed from dontrun to donttest
- filter_missing: unwrapped (takes less than 1s)
- make_seq_mappoly: changed from dontrun to donttest
- rf_snp_filter: changed from dontrun to donttest
There isn't any remaining function with \dontrun{}
Check package tests for all \donttest{} examples. Processes can not spawn in multiple cores during this step. Then, the example below was removed from est_pairwise_rf. It wouldn't be possible to achieve the desired goals without multiple-core processing. Also, the tetraploid example was changed to include only the first chromosome.
Removed example:
## Hexaploid example
fl = "https://github.com/mmollina/MAPpoly_vignettes/raw/master/data/BT/sweetpotato_chr1.vcf.gz"
tempfl <- tempfile(pattern = 'chr1_', fileext = '.vcf.gz')
download.file(fl, destfile = tempfl)
dat.dose.vcf = read_vcf(file = tempfl, parent.1 = "PARENT1", parent.2 = "PARENT2")
## Filtering dataset by marker
dat.filt.mrk <- filter_missing(input.data = dat.dose.vcf,
type = "marker",
filter.thres = 0.10,
inter = FALSE)
## Filtering dataset by individual
dat.filt.ind <- filter_missing(input.data = dat.filt.mrk,
type = "individual",
filter.thres = 0.10,
inter = FALSE)
## Segregation test
pval.bonf <- 0.05/dat.filt.ind$n.mrk
mrks.chi.filt <- filter_segregation(dat.filt.ind,
chisq.pval.thres = pval.bonf,
inter = FALSE)
seq.ch1<-make_seq_mappoly(mrks.chi.filt)
plot(seq.ch1)
## will take ~ 19 min / peak of memory usage ~ 10GB
all.pairs.1 <- est_pairwise_rf(input.seq = seq.ch1,
ncpus = 7,
verbose=TRUE)
## same thing, but it will take ~ 21 min / peak of memory usage ~ 6GB
all.pairs.2 <- est_pairwise_rf(input.seq = seq.ch1,
ncpus = 7,
n.batch = 10,
verbose=TRUE)
plot(all.pairs.1, 161, 162)
mat <- rf_list_to_matrix(all.pairs.1)
plot(mat)
Also removed this from function make_seq_mappoly (in make_seq.R):
## Making a sequence using the intersection between groups and genomic information
s <- make_seq_mappoly(tetra.solcap, 'all')
tpt <- est_pairwise_rf(input.seq = s,
ncpus = 7)
mat <- rf_list_to_matrix(tpt)
grs <- group_mappoly(input.mat = mat,
expected.groups = 12,
comp.mat = FALSE)
seq1 = make_seq_mappoly(grs, arg = 1, genomic.info = 1)
Changed number of cores from 7 to 1 in function est_rf_hmm_sequential (in est_map_hmm.R)
Changed number of cores from 7 to 1 in function make_pairs_mappoly (in make_pairs.R)
Changed number of cores from 7 to 1 and arg="all" to arg="seq1" in function rf_list_to_matrix (in rf_list_to_matrix.R)
In file import_from_polymapR.R, changed ncpus from 7 to 1 and replaced the following code:
#### Reestimating recombination fractions using HMM
cl <- parallel::makeCluster(5)
parallel::clusterEvalQ(cl, require(mappoly))
parallel::clusterExport(cl, "mappoly.data")
reest.maps <- parallel::parLapply(cl, mappoly.maplist,
est_full_hmm_with_global_error,
error = 0.05)
parallel::stopCluster(cl)
by this:
reest.maps <- lapply(mappoly.maplist,
est_full_hmm_with_global_error,
error = 0.05)
Also replaced this:
cl <- parallel::makeCluster(5)
parallel::clusterEvalQ(cl, require(mappoly))
parallel::clusterExport(cl, "mappoly.data")
recons.maps <- parallel::parLapply(cl, MAPs,
est_full_hmm_with_global_error,
error = 0.05)
parallel::stopCluster(cl)
by this:
recons.maps <- lapply(MAPs,
est_full_hmm_with_global_error,
error = 0.05)
Another error: "T used instead of TRUE"
Searched and fixed this kind of occurrence on all examples.
Also changed number of cores in import_from_updog function example (in import_from_updog.R) and removed this section:
mydata = import_from_updog(mout, filter.non.conforming = TRUE)
mydata
plot(mydata)
Bug detected when running untested examples:
- function plot.mappoly.homoprob (homolog_probs.R) line 131: changed if(lg=="all") to if(all(lg=="all")) to fix a problem when passing a vector of chromosomes as lg argument
- function plot.mappoly.homoprob (homolog_probs.R): added verbose parameter
- function plot.mappoly.homoprob (homolog_probs.R) lines 116 and 139: check for verbosity
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