Man pages for facilebio/FacileData
A fluent API for accessing multi-assay high-throughput genomics data
| adata | Bioc-container specific assay data extraction functions |
| addFacileAssaySet | Adds new set of assay data for all samples in a FacileDataSet |
| an_fds | Retrieves a multi-modal FacileDataSet based on KPMP data. |
| append_facile_feature_info | Appends new features to 'feature_info' table |
| append_facile_table | Adds rows to a table in a FacileDataSet |
| as.BiocContainer | Converts a "facile result" to a traditional Bioconductor... |
| as.EAVtable | Convert a 'pData' data.frame to a melted EAV table |
| as.FacileDataSet | Converts a (list of) bioconductor assay containers into a... |
| as_facile_frame | Converts a normal tibble/data.frame to a facile_frame |
| assay_feature_type | Returns the feature_type for a given assay |
| assay_info | Fetches assay meta information for the assays stored in a... |
| assay_sample_info | Retrieve assay-specific metadata for a set of samples |
| assay_summary | Identify the number of each assay run across specific... |
| assay_units | Units of measure in an assay |
| assemble_example_dataset | Assembles an example facile dataset to play with |
| assembleFacileDataSet | Creata a FacileDataSet from the individual assay lists |
| assertions | Check to see that samples are referenced correctly |
| biocbox | Materialize a Bioconductor assay container from some facile... |
| build_assay_list_file_path | Returns the filepath for the raw assay data for a given... |
| build_assay_lists_load | Loads an assay list object |
| build_available_assays | Description of available assays in this packge |
| build_pb_split | Splits a SingleCellExperiment in a list of DGELists, split by... |
| cast_covariate | Casts the character EAV values to their R-native defined... |
| check_categorical | Check to see if a vector is categorical (character or string) |
| check_facile_data_set | Check if argument is a FacileDataSet |
| check_facile_data_store | Check if argument is a FacileDataStore |
| conform_data_frame | Arranges the columns of one data.frame to another |
| covariate_definitions | Get description of sample metadata columns |
| covariate_meta_info | Retrieve the meta information about a covariate for EAV... |
| create_assay_feature_descriptor | Creates a feature descriptor for interactive ease |
| cSurv | cSurv is a character representation of survival::surv ### |
| dbfn | Get location of the FacileDataSet database |
| dot-level_biotypes | Utility function to "factorize" biotypes into an order we... |
| dot-prepare_sample_covariates | Helper function when creating or appending to a faciledatsets |
| ds_annot | Bioc-container specific data set annotation extraction... |
| eavdef_for_column | Generate entity-attribute-value definition for a column in a... |
| eav_encode | Encodes column(s) from 'pData' into character values |
| eav_encode_covariate | Encodes column(s) from 'pData' into character values |
| eav-metadata | Create a facile covariate definition file from a sample... |
| eav_metadata_merge | Merge inferred and explicit covariate column metadata. |
| eav-right-censor | Entity-attribute-value encodings for survival data. |
| exampleFacileDataSet | Retrieves an example FacileDataSet |
| executeSQL | Execute multiple queries against a database |
| extract_transcribed_info_from_ensembl_gtf | Extract gene- and transcript-level information from an... |
| facet_frame | Retrieves grouping table for samples within a FacileDataSet. |
| FacileData-package | FacileData: A fluent API for accessing multi-assay... |
| FacileDataSet | Instantiates a FacileDataSet object from disk. |
| facilitate | Converts an arbitrary object into one that works in the... |
| fdata | BioC-container specific fData extraction functions |
| fds | Get or set the FacileDataStore for an object |
| feature_name_map | Returns table of names and aliases for features. |
| features | Returns a table of information about the features (from an... |
| feature_types | Enumerate the types of feature stored in a FacileDataSet |
| fetch_assay_data | Fetch assay data from single assay of choice |
| fetch_assay_score | NOTE: is fetch_assay_score really necessary? |
| fetch_assay_score.FacileDataSet | Helper function to get sample assay data from single or... |
| fetch_custom_sample_covariates.FacileDataSet | Fetches custom (user) annotations for a given user prefix |
| fetch_samples.FacileDataSet | Fetches a sample descriptor that matches the filter criterion |
| fetch_sample_statistics | NOTE: fetch_sample_statistics -> 'fetch_assay_covariates'... |
| fetch_sample_statistics.default | Issue #2 |
| fetch_sample_statistics.FacileDataSet | Fetch the sample statistics for sets of samples in the... |
| filter_by_assay_support | Removes samples without specific assay support |
| filter_features.FacileDataSet | Filter against the sample_covariate_tbl as if it were wide. |
| filter_samples.FacileDataSet | Filter against the sample_covariate_tbl EAV table as if it... |
| flog | Generates a logging message using glue and crayon, with some... |
| flog_level | Retrieves the currently set logging level |
| freplace_na | Replaces NA's with specified values. |
| gene_info_tbl.FacileDataSet | Mimics the old 'gene_info' table. |
| has_assay | Checks facile objects to see if they have a particular assay... |
| has_feature_type | Test if a given feature type is stored in a FacileDataSet |
| hdf5fn | Get location of the FacileDataSet HDF5 file |
| infer_feature_type | Guesses the type of feature identifiers from a character... |
| initializeFacileDataSet | Create an empty FacileDataSet |
| is.FacileDataSet | Class and validity checker for FacileDataSet |
| join_samples | Filters the samples down in a dataset to ones specified |
| labeled | Labeled acts like interface to reactive modules. |
| meta-info | Path to the meta information YAML file |
| nameit | Ensures that a vector has names for all elements if it has... |
| normalize_assay_data | Helper functions to normalize assay data into log2 space. |
| organism.FacileDataSet | Retrieves the organism the data is defined over |
| parse_sample_criterion | Creates a filter expression to select samples based on value... |
| pdata | Bioc-container specific pData extraction functions |
| pdata_metadata | Bioc-container specific pData extraction functions |
| primary_key | Query a table to identify its primary key(s) |
| reexports | Objects exported from other packages |
| remove_batch_effect | Regress out confounding variables from a data matrix. |
| sample-covariates | Appends covariate columns to a query result |
| sample_covariate_summary | Provides a tibble summary of the covariates available over a... |
| samples | Returns a facile_frame of samples from an object in the... |
| samples.FacileDataSet | Retrieves the sample identifiers for all samples in a... |
| save_custom_sample_covariates | Saves custom sample covariates to a FacileDataSet |
| set_class | Set the class of an object and return the object |
| simple-eav-decode-functions | Entity-attribute-value decoding for real values. |
| some_celltypes | A set of cell types that exhibit strong expression... |
| some_features | A set of features that show variable expression across... |
| some_samples | Retrieve a set of samples for testing |
| spread_assay_data | Takes a result from fetch_expression and spreads out genes... |
| spread_covariates | Spreads the covariates returned from database into wide... |
| sqlFromFile | Utility function to send more than one sql command to the... |
| summary.eav_covariates | Provides a summary table of sample covariates. |
| test-helpers | Fetches exemplar data for unit testing |
| validate_covariate_def_list | Validates that a covariate defintion list reasonably... |
| with_feature_info | Append feature information columns to (feature-rows) |
