Man pages for ethanmoyer/MethylConstruct

add_dataAdd to probe-node matrix at a new node
betas_to_consensus_vectorConverts betas matrix to consensus vectors of probes for each...
create_consensus_vectorCreate consensus vector of probes for each group VALIDATED
create_node_matrixNode matrix used for tree walking VALIDATED
cut_treeRecursively walk through tree and remove descendants.
fit_betas_to_distributionCategorize betas based on bimodal distribution VALIDATED
generate_bimodal_distributionGenerate bimodal distribution VALIDATED
generate_branch_changesRelevant probes for gain, loss, and change in methylation...
generate_probe_node_matrixFully generate probe-node matrix with available data...
get_leavesLeaves of a tree
get_probes_of_geneProbes along a given gene VALIDATED
get_referenceReturns reference file VALIDATED
get_relevant_genesRelevant genes for gain and loss of methylation VALIDATED
get_rootRoot of a tree VALIDATED
grow_off_leafGrow a tree at a given leaf node
inherit_parental_stateInherit parental states to ambiguous nodes VALIDATED
initialize_probe_node_matrixInitialize the probe-node matrix VALIDATED
ninternal_nodesNumber of internal nodes on a tree VALIDATED
nleavesNumber of leaves of a tree
nnodesTotal number of nodes on a tree VALIDATED
nprobesNumber of probes in data VALIDATED
read_IDATLoad beta data
reconstruct_internal_nodesReconstruct internal nodes VALIDATED
relabel_node_matrixRelabel node in probe-node matrix
relabel_treeRelabel node on tree
remove_branches_from_nodeCut tree at specified node
remove_cell_typesRemove specific cell types from betas matrix VALIDATED
remove_intermediate_probesRemoves intermediate probes VALIDATED
remove_NA_probesRemoves NA probes VALIDATED
remove_sex_chrRemove probes on sex chromosomes VALIDATED
remove_unapplicable_probesRemoves all inapplicable probes VALIDATED
remove_zero_parsimony_probesRemoves zero parsimony probes VALIDATED
save_dataSaves specified data with variable name to working directory...
show_gene_trackTrack the single probe resolution change of a gene
show_heatmapRelabel node in probe-node matrix
show_treeDisplay tree VALIDATED
track_geneProportion of probes methylated, unmethylated, ambiguous at...
upgma_treeUPGMA tree construction VALIDATED
ethanmoyer/MethylConstruct documentation built on July 10, 2020, 12:28 a.m.