acum |
Perform gaussian sum |
add_marker |
Creates a new sequence by adding markers. |
add_redundants |
Add the redundant markers removed by create_data_bins function |
Bonferroni_alpha |
Calculates individual significance level to be used to achieve a global alpha (with Bonferroni) |
check_data |
Onemap object sanity check |
check_twopts |
Twopts object sanity check |
combine_onemap |
Combine OneMap datasets |
compare |
Compare all possible orders (exhaustive search) for a given sequence of markers |
create_dataframe_for_plot_outcross |
Create a dataframe suitable for a ggplot2 graphic |
create_data_bins |
New dataset based on bins |
create_depths_profile |
Create database and ggplot graphic of allele reads depths |
create_probs |
Build genotype probabilities matrix for hmm |
draw_map |
Draw a genetic map |
draw_map2 |
Draw a linkage map |
drop_marker |
Creates a new sequence by dropping markers. |
empty_onemap_obj |
Produce empty object to avoid code break. Function for internal purpose. |
extract_depth |
Extract allele counts of progeny and parents of vcf file |
filter_2pts_gaps |
Filter markers based on 2pts distance |
filter_missing |
Filter markers according with a missing data threshold |
filter_prob |
Function filter genotypes by genotype probability |
find_bins |
Allocate markers into bins |
generate_overlapping_batches |
Function to divide the sequence in batches with user defined size |
group |
Assign markers to linkage groups |
group_seq |
Assign markers to preexisting linkage groups |
group_upgma |
Assign markers to linkage groups |
haldane |
Apply Haldane mapping function |
keep_only_selected_mks |
Keep in the onemap and twopts object only markers in the sequences |
kosambi |
Apply Kosambi mapping function |
make_seq |
Create a sequence of markers based on other OneMap object types |
map |
Construct the linkage map for a sequence of markers |
mapmaker_example_f2 |
Simulated data from a F2 population |
map_avoid_unlinked |
Repeat HMM if map find unlinked marker |
map_overlapping_batches |
Mapping overlapping batches |
map_save_ram |
Perform map using background objects with only selected markers. It saves ram memory during the procedure. It is useful if dealing with many markers in total data set. |
marker_type |
Informs the segregation patterns of markers |
mds_onemap |
OneMap interface with MDSMap package with option for multipoint distances estimation |
onemap_example_bc |
Simulated data from a backcross population |
onemap_example_f2 |
Simulated data from a F2 population |
onemap_example_out |
Data from a full-sib family derived from two outbred parents |
onemap_example_riself |
Simulated data from a RIL population produced by selfing. |
onemap_read_vcfR |
Convert vcf file to onemap object |
order_seq |
Search for the best order of markers combining compare and try_seq functions |
parents_haplotypes |
Generates data.frame with parents estimated haplotypes |
pick_batch_sizes |
Picking optimal batch size values |
plot.onemap |
Draw a graphic of raw data for any OneMap population |
plot.onemap_progeny_haplotypes |
Plots progeny haplotypes |
plot.onemap_progeny_haplotypes_counts |
Plot recombination breakpoints counts for each individual |
plot.onemap_segreg_test |
Plot p-values for chi-square tests of expected segregation |
plot_by_segreg_type |
Draw a graphic showing the number of markers of each segregation pattern. |
print.compare |
print method for object class 'compare' |
print.onemap |
Print method for object class 'onemap' |
print.onemap_bin |
print method for object class 'onemap_bin' |
print.onemap_segreg_test |
Show the results of segregation tests |
print.order |
Print order_seq object |
print.sequence |
Print method for object class 'sequence' |
progeny_haplotypes |
Generate data.frame with genotypes estimated by HMM and its probabilities |
progeny_haplotypes_counts |
Plot number of breakpoints by individuals |
rcd |
Rapid Chain Delineation |
read_mapmaker |
Read data from a Mapmaker raw file |
read_onemap |
Read data from all types of progenies supported by OneMap |
record |
Recombination Counting and Ordering |
remove_inds |
Remove individuals from the onemap object |
rf_2pts |
Two-point analysis between genetic markers |
rf_graph_table |
Plots pairwise recombination fractions and LOD Scores in a heatmap |
rf_snp_filter_onemap |
Filter markers according with a two-points recombination fraction and LOD threshold. Adapted from MAPpoly. |
ripple_seq |
Compares and displays plausible alternative orders for a given linkage group |
rm_dupli_mks |
Remove duplicated markers keeping the one with less missing data |
seeded_map |
Construct the linkage map for a sequence of markers after seeding phases |
select_segreg |
Show markers with/without segregation distortion |
seq_by_type |
Extract marker number by name |
seriation |
Seriation |
set_map_fun |
Defines the default mapping function |
sort_by_pos |
Sort markers in onemap object by their position in reference genome |
split_2pts |
Split rf_2pts object by markers |
split_onemap |
Split onemap data sets |
suggest_lod |
Suggests a LOD Score for two point tests |
test_segregation |
test_segregation |
test_segregation_of_a_marker |
test_segregation_of_a_marker |
try_seq |
Try to map a marker into every possible position between markers in a given map |
try_seq_by_seq |
Run try_seq considering previous sequence |
ug |
Unidirectional Growth |
vcf2raw |
These functions are defunct and no longer available. |
vcf_example_bc |
Data generated from VCF file with biallelic markers from a f2 backcross population |
vcf_example_f2 |
Data generated from VCF file with biallelic markers from a f2 intercross population |
vcf_example_out |
Data generated from VCF file with biallelic markers from a full-sib family derived from two outbred parents |
vcf_example_riself |
Data generated from VCF file with biallelic markers from a RIL population produced by selfing |
write_map |
Write a genetic map to a file |
write_onemap_raw |
Convert onemap object to onemap raw file |