CompassSettings: CompassSettings
In YosefLab/compassR: A Library for Conducting Analyses on COMPASS Data
Description
Public fields
Methods
Description
An object through which you can specify settings for your COMPASS analysis.
Public fields
gene_metadata_pathA path to a file containing tabular gene metadata. Each row should represent a single gene. The columns are up to you, so long as one of them provides a unique identifier for each gene.
metabolite_metadata_pathA path to a file containing tabular metabolite metadata. Each row should represent a single metabolite. The columns are up to you, so long as one of them provides a unique identifier for each metabolite.
reaction_metadata_pathA path to a file containing tabular reaction metadata. Each row should represent a single reaction. The columns are up to you, so long as one of them provides a unique identifier for each reaction.
cell_metadata_pathA path to a file containing tabular cell metadata. Each row should represent a single cell. The columns are up to you, so long as one of them provides a unique identifier for each cell.
compass_reaction_scores_pathA path to a file containing the raw reaction consistencies matrix. (This is the output of the COMPASS algorithm.)
linear_gene_expression_matrix_pathA path to a file containing the linear gene expression matrix. (This is the input to the COMPASS algorithm.)
cell_id_col_nameThe name of the column that uniquely identifies each cell in the cell metadata file.
gene_id_col_nameThe name of the column that uniquely identifies each gene in the gene metadata file.
reaction_direction_separatorIt is assumed that reaction IDs take the form unique idseparatorone of N annotations, where the separator is specified by this length-1 character vector, interpreted as a regular expression.
reaction_directionsIt is assumed that reaction IDs take the form unique idseparatorone of N annotations, where the annotations are specified by this length-N character vector, interpreted as regular expressions.
min_reaction_consistencyReactions are dropped that have consistency scores below this threshold.
min_reaction_rangeReactions are dropped that have a range of consistency scores narrow than this threshold.
cluster_strengthA number between 0 and 1, specifying the aggressiveness with which to cluster similar reactions together into metareactions.
Methods
Public methods
Method new()
Description.
Usage
CompassSettings$new(
...,
metabolic_model_directory = system.file("extdata", "RECON2", package = "compassR",
mustWork = TRUE),
gene_metadata_file = "gene_metadata.csv",
metabolite_metadata_file = "metabolite_metadata.csv",
reaction_metadata_file = "reaction_metadata.csv",
user_data_directory,
cell_metadata_file = "cell_metadata.csv",
compass_reaction_scores_file = "reactions.tsv",
linear_gene_expression_matrix_file = "linear_gene_expression_matrix.tsv",
cell_id_col_name,
gene_id_col_name,
reaction_direction_separator = "_",
reaction_directions = c("pos", "neg"),
min_reaction_consistency = 1e-04,
min_reaction_range = 1e-08,
cluster_strength = 0.1
)
Arguments
...Unused.
metabolic_model_directoryThe path to the directory containing the specifications of your metabolic model.
gene_metadata_fileA path to a file in the metabolic_model_directory containing tabular gene metadata. Each row should represent a single gene. The columns are up to you, so long as one of them provides a unique identifier for each gene.
metabolite_metadata_fileA path to a file in the metabolic_model_directory containing tabular metabolite metadata. Each row should represent a single metabolite. The columns are up to you, so long as one of them provides a unique identifier for each metabolite.
reaction_metadata_fileA path to a file in the metabolic_model_directory containing tabular reaction metadata. Each row should represent a single reaction. The columns are up to you, so long as one of them provides a unique identifier for each reaction.
user_data_directoryThe path to the directory containing the data specific to the analysis you hope to conduct.
cell_metadata_fileA path to a file in the user_data_directory containing tabular cell metadata. Each row should represent a single cell. The columns are up to you, so long as one of them provides a unique identifier for each cell.
compass_reaction_scores_fileA path to a file in the user_data_directory containing the raw reaction consistencies matrix. (This is the output of the COMPASS algorithm.)
linear_gene_expression_matrix_fileA path to a file in the user_data_directory containing the linear gene expression matrix. (This is the input to the COMPASS algorithm.)
cell_id_col_nameThe name of the column that uniquely identifies each cell in the cell metadata file.
gene_id_col_nameThe name of the column that uniquely identifies each gene in the gene metadata file.
reaction_direction_separatorIt is assumed that reaction IDs take the form unique idseparatorone of N annotations, where the separator is specified by this length-1 character vector, interpreted as a regular expression.
reaction_directionsIt is assumed that reaction IDs take the form unique idseparatorone of N annotations, where the annotations are specified by this length-N character vector, interpreted as regular expressions.
min_reaction_consistencyReactions are dropped that have consistency scores below this threshold.
min_reaction_rangeReactions are dropped that have a range of consistency scores narrow than this threshold.
cluster_strengthA number between 0 and 1, specifying the aggressiveness with which to cluster similar reactions together into metareactions.
Returns
NULL.
Method print()
Prints a human-readable representation of this CompassSettings instance.
Usage
CompassSettings$print(...)
Arguments
...Unused.
Returns
NULL.
Method repr()
Returns a human-readable representation of this CompassSettings instance.
Usage
CompassSettings$repr(...)
Arguments
...Unused.
Returns
An output.
Method clone()
The objects of this class are cloneable with this method.
Usage
CompassSettings$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
YosefLab/compassR documentation built on May 3, 2021, 7:31 a.m.
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Description Public fields Methods
Description
An object through which you can specify settings for your COMPASS analysis.
Public fields
gene_metadata_pathA path to a file containing tabular gene metadata. Each row should represent a single gene. The columns are up to you, so long as one of them provides a unique identifier for each gene.
metabolite_metadata_pathA path to a file containing tabular metabolite metadata. Each row should represent a single metabolite. The columns are up to you, so long as one of them provides a unique identifier for each metabolite.
reaction_metadata_pathA path to a file containing tabular reaction metadata. Each row should represent a single reaction. The columns are up to you, so long as one of them provides a unique identifier for each reaction.
cell_metadata_pathA path to a file containing tabular cell metadata. Each row should represent a single cell. The columns are up to you, so long as one of them provides a unique identifier for each cell.
compass_reaction_scores_pathA path to a file containing the raw reaction consistencies matrix. (This is the output of the COMPASS algorithm.)
linear_gene_expression_matrix_pathA path to a file containing the linear gene expression matrix. (This is the input to the COMPASS algorithm.)
cell_id_col_nameThe name of the column that uniquely identifies each cell in the cell metadata file.
gene_id_col_nameThe name of the column that uniquely identifies each gene in the gene metadata file.
reaction_direction_separatorIt is assumed that reaction IDs take the form unique idseparatorone of N annotations, where the separator is specified by this length-1 character vector, interpreted as a regular expression.
reaction_directionsIt is assumed that reaction IDs take the form unique idseparatorone of N annotations, where the annotations are specified by this length-N character vector, interpreted as regular expressions.
min_reaction_consistencyReactions are dropped that have consistency scores below this threshold.
min_reaction_rangeReactions are dropped that have a range of consistency scores narrow than this threshold.
cluster_strengthA number between 0 and 1, specifying the aggressiveness with which to cluster similar reactions together into metareactions.
Methods
Public methods
Method new()
Description.
Usage
CompassSettings$new(
...,
metabolic_model_directory = system.file("extdata", "RECON2", package = "compassR",
mustWork = TRUE),
gene_metadata_file = "gene_metadata.csv",
metabolite_metadata_file = "metabolite_metadata.csv",
reaction_metadata_file = "reaction_metadata.csv",
user_data_directory,
cell_metadata_file = "cell_metadata.csv",
compass_reaction_scores_file = "reactions.tsv",
linear_gene_expression_matrix_file = "linear_gene_expression_matrix.tsv",
cell_id_col_name,
gene_id_col_name,
reaction_direction_separator = "_",
reaction_directions = c("pos", "neg"),
min_reaction_consistency = 1e-04,
min_reaction_range = 1e-08,
cluster_strength = 0.1
)Arguments
...Unused.
metabolic_model_directoryThe path to the directory containing the specifications of your metabolic model.
gene_metadata_fileA path to a file in the metabolic_model_directory containing tabular gene metadata. Each row should represent a single gene. The columns are up to you, so long as one of them provides a unique identifier for each gene.
metabolite_metadata_fileA path to a file in the metabolic_model_directory containing tabular metabolite metadata. Each row should represent a single metabolite. The columns are up to you, so long as one of them provides a unique identifier for each metabolite.
reaction_metadata_fileA path to a file in the metabolic_model_directory containing tabular reaction metadata. Each row should represent a single reaction. The columns are up to you, so long as one of them provides a unique identifier for each reaction.
user_data_directoryThe path to the directory containing the data specific to the analysis you hope to conduct.
cell_metadata_fileA path to a file in the user_data_directory containing tabular cell metadata. Each row should represent a single cell. The columns are up to you, so long as one of them provides a unique identifier for each cell.
compass_reaction_scores_fileA path to a file in the user_data_directory containing the raw reaction consistencies matrix. (This is the output of the COMPASS algorithm.)
linear_gene_expression_matrix_fileA path to a file in the user_data_directory containing the linear gene expression matrix. (This is the input to the COMPASS algorithm.)
cell_id_col_nameThe name of the column that uniquely identifies each cell in the cell metadata file.
gene_id_col_nameThe name of the column that uniquely identifies each gene in the gene metadata file.
reaction_direction_separatorIt is assumed that reaction IDs take the form unique idseparatorone of N annotations, where the separator is specified by this length-1 character vector, interpreted as a regular expression.
reaction_directionsIt is assumed that reaction IDs take the form unique idseparatorone of N annotations, where the annotations are specified by this length-N character vector, interpreted as regular expressions.
min_reaction_consistencyReactions are dropped that have consistency scores below this threshold.
min_reaction_rangeReactions are dropped that have a range of consistency scores narrow than this threshold.
cluster_strengthA number between 0 and 1, specifying the aggressiveness with which to cluster similar reactions together into metareactions.
Returns
NULL.
Method print()
Prints a human-readable representation of this CompassSettings instance.
Usage
CompassSettings$print(...)
Arguments
...Unused.
Returns
NULL.
Method repr()
Returns a human-readable representation of this CompassSettings instance.
Usage
CompassSettings$repr(...)
Arguments
...Unused.
Returns
An output.
Method clone()
The objects of this class are cloneable with this method.
Usage
CompassSettings$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
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