kpm_options: Set or get options for KeyPathwayMineR

In baumbachlab/keypathwayminer-R: KeyPathwayMiner R-Package

Set or get options for KeyPathwayMineR

Description

Set or get options for KeyPathwayMineR

Usage

kpm_options(...)

Arguments

...

Option names to retrieve option values or [key]=[value] pairs to set options. Default parameters: kpm_options(execution = "Local", async = TRUE, url = "https://exbio.wzw.tum.de/keypathwayminer/", algorithm = "Greedy", graph_id = 1, strategy = "GLONE", remove_bens = FALSE, use_range_k = FALSE, k_min = 1, k_max = 3, k_step = 1, use_range_l = FALSE, l_min =0, l_max = 0, l_step = 1, l_same_percentage = FALSE, same_percentage = 0, computed_pathways = 20, perturbation_start = 10, perturbation_step = 10, perturbation_max = 20, graphs_per_step = 1, with_perturbation = FALSE, perturbation_technique = "nodeswap", unmapped_nodes = "Add to negative list", link_type = "OR", properties_file = "kpm.properties", matrix_header = FALSE, negative_nodes, positive_nodes)

I. Options for remote and local use

• execution ("Local" or "Remote") Execution type of KeyPathwayMineR. Either via RestfulAPI or standalone jar

• algorithm ("Greedy", "ACO", "Optimal") The algorithm that will be used to extract the pathways

• strategy ("GLONE", "INES") The strategy that will be used to extract pathways

• remove_bens (Boolean) If TRUE border exception nodes will be removed

• computed_pathways (Integer) The number of solutions that should be computed

• link_type ("OR", "AND") Define how multiple datasets should be combined in the analysis

• matrix_header (Boolean) TRUE if input matrices have a header (Case/Sample description). FALSE if not.

Gene exceptions K (only used for INES):

• use_range_k (Boolean) If TRUE k_values will be ranged (batch run). If false the user only needs to set k_min.

• k_min (Integer) Starting value of k range or k value if k is not ranged

• k_step (Integer) How k should be increased within the range

• k_max (Integer) The maximum k value, i.e. the upper limit of the range

The case (L) exceptions for the n-th matrix:

• use_range_l (Boolean) If TRUE l_values will be ranged (batch run). If false the user only needs to set l_min

• l_min (Integer) Starting value of l range or l value if l is not ranged

• l_step (Integer) How l should be increased within the range

• l_max (Integer) The maximum l value, i.e. the upper limit of the range

II. Parameters only for remote execution

• async (Boolean)
  TRUE = Submit job asynchronously (returns immediately)
  FALSE = Submit a new job am (returns when job is complete)

• session_id (String) The id of the job to be queried

• url (String) URL for HTTP request

• graph_id (Integer) The id of one of the networks that are available when you call get_networks()

• unmapped_nodes ("Add to negative list", "Add to positive list") String What should be done with unmapped nodes, i.e. should they be added to the positive list (always included in solutions) or to the negative list (categorically ignored)

• l_same_percentage (Boolean) If multiple datasets are defined, should the same l value be used for all of them

• same_percentage (Percentage 0:100) The l percentage value that should be used for multiple datasets

III. Parameters only for local execution

• properties_file (String) Path to properties file

Options for network robustness analysis:

• with_perturbation (Boolean) Set TRUE to perform a robustness analysis

• perturbation_technique ('edgeremove', 'edgerewire', 'nodeswap') Perturbation technique to use for the analysis

• perturbation_start (Integer) Perturbation percentage range lower value

• perturbation_step (Integer) Perturbation percentage step size

• perturbation_max (Integer) Perturbation percentage range upper value

• graphs_per_step(Integer) Number of random graphs to be created (permutations)

• positive_nodes(Character vector) Vector of node ids that should be considered active)

• negative_nodes(Character vector) Vector of node ids that should be considered inactive)

baumbachlab/keypathwayminer-R documentation built on June 29, 2023, 11:21 a.m.