Man pages for PavlidisLab/Gemma-API
A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses
| accessField | Access the field in a list |
| blank_processor | A blank processor that returns data as is |
| checkBounds | Replace missing data with NAs |
| dot-getResultSets | Retrieve a single analysis result set by its identifier |
| encode | URL encode a string safely |
| filter_properties | Return all supported filter properties |
| forget_gemma_memoised | Clear gemma.R cache |
| gemmaCache | Gemma Cache |
| gemma_call | Custom gemma call |
| gemma_kable | Create printable tables out of gemma.R outputs |
| gemma_memoise | Enable and disable memoisation of gemma.R functions |
| gemmaPath | Get gemma path |
| gemma.R | gemma.R package: Access curated gene expression data and... |
| get_all_pages | Get all pages of a paginated call |
| get_child_terms | Return child terms of a term |
| get_dataset_annotations | Retrieve the annotations of a dataset |
| get_dataset_design | Retrieve the design of a dataset |
| get_dataset_differential_expression_analyses | Retrieve annotations and surface level stats for a dataset's... |
| get_dataset_expression | Retrieve processed expression data of a dataset |
| get_dataset_expression_for_genes | Retrieve the expression data matrix of a set of datasets and... |
| get_dataset_object | Compile gene expression data and metadata |
| get_dataset_platforms | Retrieve the platforms of a dataset |
| get_dataset_processed_expression | Retrieve processed expression data of a dataset |
| get_dataset_quantitation_types | Retrieve quantitation types of a dataset |
| get_dataset_raw_expression | Retrieve raw expression data of a dataset |
| get_datasets | Retrieve all datasets |
| get_dataset_samples | Retrieve the samples of a dataset |
| get_datasets_by_ids | Retrieve datasets by their identifiers |
| get_differential_expression_values | Retrieve differential expression results |
| get_gene_differential_expression_values | Retrieve the differential expression results for a given gene... |
| get_gene_go_terms | Retrieve the GO terms associated to a gene |
| get_gene_locations | Retrieve the physical locations of a given gene |
| get_gene_probes | Retrieve the probes associated to a genes across all... |
| get_genes | Retrieve genes matching gene identifiers |
| get_platform_annotations | Retrieve Platform Annotations by Gemma |
| get_platform_datasets | Retrieve all experiments using a given platform |
| get_platform_element_genes | Retrieve the genes associated to a probe in a given platform |
| get_platforms_by_ids | Retrieve all platforms matching a set of platform identifiers |
| get_result_sets | Retrieve all result sets matching the provided criteria |
| get_taxa | Get taxa |
| get_taxa_by_ids | Retrieve taxa by their identifiers |
| get_taxon_datasets | Retrieve the datasets for a given taxon |
| isEmpty | Check for empty arguments |
| make_design | Make simplified design frames |
| memoise | Memoise doc |
| nullCheck | Avoid NULLS as data.table columns |
| processAnnotations | Processes JSON as annotations |
| processCharacteristicValueObject | Processes JSON as a factor |
| processDatasetResultSets | Processes JSON as a datasets result set |
| processDatasets | Processes JSON as a vector of datasets |
| processDEA | Processes JSON as a differential expression analysis |
| processDEcontrasts | Replaces factor ids by the factors strings in DE table... |
| processDEMatrix | Processes differential expression matrix |
| processDesignMatrix | Processes design matrix |
| processDifferentialExpressionAnalysisResultByGeneValueObject_tsv | processDifferentialExpressionAnalysisResultByGeneValueObject_tsv |
| processDifferentialExpressionAnalysisResultSetValueObject | Process JSON of a result set |
| processElements | Processes JSON as a vector of elements |
| processExpressionMatrix | Processes expression matrix |
| processFile | Processes a response as a gzip file |
| processGemmaArray | Processes JSON as an array |
| processGeneLocation | Processes JSON as a vector of gene locations |
| processGenes | Processes JSON as a vector of genes |
| processGO | Processes JSON as GO terms |
| processPlatforms | Processes JSON as a vector of platforms |
| processQuantitationTypeValueObject | processQuantitationTypeValueObject |
| processResultSetFactors | Processes JSON as a result set |
| processSamples | Processes JSON as a vector of samples |
| process_search | Returns the ids of the found results |
| processSearchAnnotations | Processes JSON as an annotation |
| processTaxon | Processes JSON as a vector of taxa |
| search_annotations | Search for annotation tags |
| search_datasets | Retrieve datasets associated to an annotation tags search |
| search_gemma | Search everything in Gemma |
| setGemmaPath | Set gemma path |
| set_gemma_user | Authentication by user name |
| subset_factorValues | Get a subset of an array of factorValues |
| update_result | Update result |
| validateBoolean | Validate a boolean value |
| validateID | Validate identifiers (ie. gene ID, platform ID, etc.) that... |
| validateLimit | Validate a limit value |
| validateOptionalID | Validate identifiers (ie. gene ID, platform ID, etc.) that... |
| validateOptionalQuery | Validate am optional query |
| validateOptionalTaxon | Validate a taxon using the acceptable taxa entries |
| validatePositiveInteger | Validate a non-negative integer value |
| validateQuery | Validate a query |
| validateResultType | Validate result types |
| validateSingleID | Validate a single identifier(ie. gene ID, platform ID, etc.) |
| validateSort | Validate a sort argument |
| validateTaxa | Validate taxa using the acceptable taxa entries |
| validateTaxon | Validate a taxon using the acceptable taxa entries |
