Man pages for stemangiola/ARMET
What the Package Does (One Line, Title Case)

add_absolute_proportions_to_treePut absolute proportions on tree
add_data_to_tree_from_tablePut proportions on tree
add_info_to_treeAdd info to tree
ARMET-packageThe 'ARMET' package.
ARMET_tcARMET-tc main
ARMET_tc_coreAlgCore algorithm
check_if_sd_zero_and_correctChecks if the standard deviation of a gene is 0
check_inputCheck the input for anomalies
create_temp_result_directoryCreates the directory needed for archive
drop_node_from_treeDrop a node from the tree
get_child_and_group_backgroundGet the right level of the tree and label the leaf
get_distributions_from_treeGet information from tree recursively for every node
get_gene_distributons_recursiveRun ARMET core algorithm recursively on the tree
get_genesGet genes from tree
get_hierarchyGet cell type hierarchy of a node
get_iniGet parameters from ini file if it exists
get_leave_labelGet any info from the tree
get_leave_namesGet leaves cell type names
get_map_foreground_backgroundCreate a map where every leaf is mapped with the right...
get_node_from_geneGet nome from gene
get_node_from_nameGet node from cell type
get_node_label_level_specficGet cell type names from a specific level of the tree
get_node_label_recursiveGet information from tree recursively for every node
parse_summary_vector_in_2DParse a vector from stan fit object in a 2D matrix
plot_densitiesPlots the densities distributions columnwise of a matrix
plot_densities_from_meltedPlots the densities from a melted data frame
prepare_inputCreate object for full bayesian model, with the reference...
quant_norm_to_targetNormalize array to match RNAseq
rnaseq_normNormalize a RNA seq data set using rnaseq_norm.calcNormFactor
rnaseq_norm.calcNormFactorCalculate the norm factor with calcNormFactor from limma
rnaseq_norm.get_cpmEliminate lowly tanscribed genes for normalization
rnaseq_norm.get_low_expressedEliminate lowly tanscribed genes for normalization
rnaseq_norm_ref_mixNormalize ref to match mix using TMM
run_coreAlg_though_treeRun ARMET core algorithm on the tree
run_coreAlg_though_tree_recursiveRun ARMET core algorithm recursively on the tree
wrapper_normalize_mix_refWrapper function for all normalization based on the current...
stemangiola/ARMET documentation built on Nov. 28, 2018, 2:12 p.m.