Man pages for uqrmaie1/admixtools
Inferring demographic history from genetic data

admixtoolsTools for inferring demographic history from genetic data
afs_to_countsCompute count blocks and write them to disk
afs_to_f2Compute f2 blocks and write them to disk
afs_to_f2_blocksCompute all pairwise f2 statistics
boo_listGenerate a list of bootstrap resampled arrays
compare_fits2Compare the fit of two qpgraph models
compare_fits3Compare the fit of two qpgraph models
compare_fits4Compare the fit of two qpgraph models
decomposed_tree_neighborsFind all trees within SPR distance of 1 of all graph...
delete_admixDelete an admixture edge
delete_groupsDelete groups
delete_leafRemove population from graph
desimplify_graphAdd two nodes before each admixture node
edges_to_igraphConvert data frame graph to igraph
eigenstrat_to_afsRead allele frequencies from _EIGENSTRAT_ files
est_to_booTurn per-block estimates into bootstrap estimates
est_to_looTurn per-block estimates into leave-one-out estimates
example_annoData frame with sample annotations
example_f2_blocksBlocked f2-statistics for 7 populations
example_graphAdmixture graph for 7 populations
example_igraphAdmixture graph for 7 populations
example_qpgraph_ref_resultsexample_graph fitted using qpGraph
example_triplesData frame with population triples
example_winnerData frame with one fitted admixture graph
example_winnersData frame with fitted admixture graphs
extract_afsCompute and store blocked allele frequency data
extract_afs_simpleCompute and store blocked allele frequency data
extract_countsExtract and store data needed to compute blocked f2
extract_f2Compute and store blocked f2 statistics
extract_f2_largeCompute and store blocked f2 statistics
extract_f2_subsetCopy f2-statistics
extract_samplesExtract samples from PLINK files
f2Estimate f2 statistics
f2_from_genoCompute blocked f2 statistics
f2_from_precompRead blocked f2 statistics from disk
f4blockdat_from_genof4 from genotype data
f4blockdat_to_f4blocksTurn f4 block data to 3d array
f4_from_f2Get per-block f4-statistics
find_admixedgesFind admixture edges
find_graphsFind well fitting admixture graphs
find_newedgesFind possible new edges
find_normedgesFind drift edges
flipadmix_randomModify a graph flipping the direction of an admixture edge
generate_all_graphsGenerate all graphs
generate_all_treesGenerate all trees
get_block_lengthsFind LD-independent blocks
get_f2Turns f2_data into f2_blocks
get_leafnamesGet the population names of a graph
get_outpopGet the outgroup from a graph (if it exists)
get_rootnameGet the root name
graph_addleafAdd a population to an admixture graph
graph_flipadmixFind all valid graphs which result from flipping one...
graph_minusoneFind all graphs which result from removing one admixture edge
graph_minusplusFind all graphs which result from adding and removing one...
graphmod_pavelReturn all graphs created from permuting a subclade
graph_plusoneFind all graphs which result from adding one admixture edge
graph_splittreesFind all trees which are part of the admixture graph
group_samplesGroup precomputed data
insert_admix_igraphInsert admixture edges into graph
insert_edgeInsert a single edge into graph
insert_edgesInsert admixture edges into graph
insert_leafAdd population to graph
isomorphism_classesFind identical graphs
isomorphism_classes2Find identical graphs
lazadmEstimate admixture weights
loo_listGenerate a list of leave-one-out arrays
loo_to_estTurn leave-one-out estimates to per-block estimates
move_admixedge_onceModify a graph by moving an admixture edge
msprime_simGenerate msprime simulation code from admixture graph
mutate_nModify a graph by applying n mutation functions
newick_to_edgesTurn a newick format tree to a matrix of edges
node_countsCount how often each node in graph occurs in other graphs
node_signatureReturns a signature of a graph consisting of the left and...
numadmixCount number of admixture nodes
packedancestrymap_to_afsRead allele frequencies from packedancestrymap files
packedancestrymap_to_plinkConvert _EIGENSTRAT_ or _PACKEDANCESTRYMAP_ to _PLINK_
parse_qp3pop_outputRead qp3Pop output file
parse_qpadm_outputRead qpAdm output file
parse_qpdstat_outputRead qpDstat output file
parse_qpf4ratio_outputRead qpF4ratio output file
parse_qpgraph_graphfileRead qpGraph graph file
parse_qpgraph_outputRead qpGraph output file
permute_leavesModify a graph by permuting leaf nodes
plink_to_afsRead allele frequencies from 'PLINK' files
plot_comparisonCompare two models
plot_graphPlot an admixture graph
plot_graph_mapPlot an admixture graph on a map
plotly_comparisonCompare two models
plotly_graphPlot an admixture graph using plotly
plot_mapPlot samples on a map
qp3popEstimate f3 statistics
qp3pop_wrapperWrapper function around the original qp3Pop program
qpadmEstimate admixture weights
qpadm_modelsReturn all valid qpAdm models for an admixturegraph
qpadm_multiRun multiple qpadm models
qpadm_pFaster version of 'qpadm' with reduced output
qpadm_rotateCompute all pairwise qpadm p-values
qpadm_wrapperWrapper function around the original qpAdm program
qpdstatEstimate f4 statistics
qpdstat_wrapperWrapper function around the original qpDstat program
qpf4ratioEstimate admixture proportions via f4 ratios
qpf4ratio_wrapperWrapper function around the original qpF4ratio program
qpgraphCompute the fit of an admixture graph
qpgraph_precompute_f3Compute f3-statistics from f2-statistics.
qpgraph_resample_multiEvaluate a qpgraph models many times
qpgraph_resample_snps2Evaluate a qpgraph model many times
qpgraph_wrapperWrapper function around the original qpGraph program
qpwaveEstimate admixture waves
qpwave_pairsCompute all pairwise qpwave p-values
random_admixturegraphGenerate a random admixture graph
random_newickGenerate a random binary graph
read_eigenstratRead genotype data from _EIGENSTRAT_ files
read_f2Read blocked f2 estimates from disk
read_packedancestrymapRead genotype data from packedancestrymap files
read_plinkRead genotype data from 'PLINK' files
resample_indsRun models while leaving out individuals
resample_snpsRun models while leaving out SNP blocks
run_shiny_admixtoolsLaunch ADMIXTOOLS 2 GUI
shortest_unique_prefixesReturn shortest unique prefixes
simplify_graphRemove redundant edges
split_matSplit a matrix into blocks
spr_allModify a graph by regrafting a subcomponent
spr_leavesModify a graph by regrafting a leaf
summarize_triplesSummarize triples across graphs
swap_leavesModify a graph by swapping two leaf nodes
test_cladalityTest if two sets of populations form two clades
tree_neighborsFind all trees within SPR distance of 1
write_dotConvert graph to dot format
write_f2Write blocked f2 estimates to disk
uqrmaie1/admixtools documentation built on Sept. 29, 2020, 1:53 a.m.