Man pages for russHyde/miiq
Microarrays Are Awesome: Get Them Analysed HERE!
| add_entrez_ids_to_esets | Function to append entrez-ids to a list of esets. The... |
| add_gpl_to_eset | add_gpl_to_eset |
| build_eset_normaliser | create a function that can normalise an ExpressionSet... |
| check_if_pretransformed_eset | Function that performs a few tests to check if a given... |
| contrast_builder | Builds a function that makes the contrast matrix for a... |
| design_builder | Builds a function that makes the design matrix for a dataset |
| DiffexConfig | Constructor function for DiffexConfig class |
| DiffexConfig-class | Class definition for DiffexConfig |
| dl_aryx_raw | Download raw data from ArrayExpress |
| dl_gds_to_gpl | Obtains the GPL accession(s) for a set of input GDS uids from... |
| dl_geo_processed | Download processed data from GEO for a GSE accession number |
| dl_geo_raw | Download raw data from GEO for a GSE accession number |
| dot-get_from_env | Obtain an object from a specific package based on a string |
| dot-make_gpl_filename | Constructs the filename for a GPL dataset |
| dot-make_gpl_url | Converts a GPL accession number into the FTP URL for that... |
| download_gpl_annotations | Download GPL-annotations from GEO for a... |
| eset_limma_dataset | Row-subsetting (feature-subsetting) operator for... |
| eset_limma_dataset-class | Class to hold ExpressionSets and limma model results |
| filter_and_transform_eset | Function that filters and transforms the entries in the... |
| geo_id_to_accession | geo_id_to_accession |
| get_or_else | get_or_else |
| get_refseq_colnames | Not exported: checks if a valid refseq column is present in... |
| get_refseq_column | Returns a RefSeq-annotation-containing column name from an... |
| gld_fnBuilder_exptDesign | Builds a function that makes the design matrix for a dataset |
| gld_fnBuilder_keepSample | Builds a function that returns the col indices of the desired... |
| gld_fnDefault_esetAnnotation | Default function for annotating the ExpressionSet with... |
| gld_fnDefault_exptDesign | Default function for setting up an expt design from the pData... |
| gld_fnDefault_keepProbe | Default function for choosing which probes to keep in an ESet... |
| gld_fnDefault_keepSample | Default function for choosing which samples to keep in a ESet... |
| gld_fnDefault_transformAndProbeFilter | Default function for transforming (etc) a microarray dataset |
| has_refseq_column | Not exported: checks if an ExpressionSet has a valid RefSeq... |
| import_aryx_affy_raw | import_aryx_affy_raw |
| import_geo_affy_raw | import_geo_affy_raw |
| import_geo_processed | import_geo_processed |
| import_gpl | import_gpl |
| inf_omit | Function to remove any infinite values from a vector |
| keep_all_entrez_probes | keep_all_entrez_probes |
| keep_all_probes | keep_all_probes: return the index for each probe on an... |
| keep_all_samples | keep_all_samples |
| keep_probe_fn | Function for filtering on microarray probes |
| limma_workflow | limma workflow: ..... |
| meta-diffex_classes-NULL-function | meta-diffex_classes-NULL-function |
| meta-extdata_download_classes-NULL-function | meta-extdata_download_classes-NULL-function |
| meta-extdata_import_classes-NULL-function | meta-extdata_import_classes-NULL-function |
| MicroarrayDownloadConfig | Sets up a class for storing the options for downloading... |
| MicroarrayDownloadConfig-class | Class definition for MicroarrayDownloadConfig |
| MicroarrayImportConfig | Sets up a class for storing the options for importing... |
| MicroarrayImportConfig-class | Class definition for MicroarrayImportConfig |
| MicroarrayPreprocessConfig | Sets up a class for storing the options for preprocessing... |
| MicroarrayPreprocessConfig-class | Class definition for MicroarrayPreprocessConfig |
| multisymbol_to_entrez_ids | multisymbol_to_entrez_ids |
| na_inf_omit | Function to remove any NA or infinite values from a vector |
| normalise_processed_eset | Take a processed ESet, eg from GEOquery, and normalise it |
| normalise_raw_affy_eset | Take newly imported affymetrix data and rma-normalise then... |
| nullFunction | nullFunction |
| paste_gene_symbols | Function to zip together a vector of entrez_ids with the gene... |
| preprocess_eset_workflow | Workflow function for converting an ExpressionSet into an... |
| run_diffex_workflow-methods | Generic for the method 'run_diffex_workflow' |
| run_download_workflow | 'run_download_workflow' method for the... |
| run_import_workflow-methods | Generic for the method 'run_import_workflow' |
| run_preprocess_workflow-methods | Generic for the method 'run_preprocess_workflow' |
| swissprot_column_to_refseq | Extract any NM_XXXX or NR_XXXX RefSeq/GenBank identifiers out... |
| symbol_to_entrez_id | Function to map gene symbols to entrez gene ids. The input... |
