Package index • rmams

Functions to manipulate rmams

convert_seurat_to_MAMS(): Converts Seurat object to a MAMS object

convert_SCE_to_MAMS(): Converts a SingleCellExperiment object to a MAMS object

convert_AnnData_to_MAMS(): Converts a AnnData object to a MAMS object

create_MAMS_from_JSON(): Create a MAMS object from a JSON file

create_MAMS_object(): Constructor function to create a MAMS object

check_MAMS(): Validate mams object

write_MAMS_to_output(): Create a JSON object from MAMS

convert_MAMS_to_list(): Convert input MAMS object to a list of list structre Useful for storing mams object into the uns slot of AnnData object

create_FEA_object(): Constructor for the FEA S4 object

create_FID_object(): Constructor for the FID S4 object

create_FNG_object(): Constructor for the FNG (feature neighborhood graph) S4 object

create_FOM_object(): Constructor function to create a FOM object

create_OBS_object(): Constructor for the OBS (observations) S4 object

create_OID_object(): Constructor for the OID S4 object

create_ONG_object(): Constructor for the ONG (observation neighborhood graph) S4 object

create_REC_object(): Constructor for the REC (provenance records) S4 object

Internal classes & functions

FEA-class: class FEA

fea(): fea

`fea<-`(): fea<-

FID-class: class FID

fid(): fid

`fid<-`(): fid<-

FNG-class: class FNG

fng(): fng

`fng<-`(): fng<-

FOM-class: class FOM

fom(): fom

`fom<-`(): fom<-

MAMS-class: class MAMS

OBS-class: class OBS

obs(): obs

`obs<-`(): obs<-

OID-class: class OID

oid(): oid

`oid<-`(): oid<-

ONG-class: class ONG

ong(): ong

`ong<-`(): ong<-

REC-class: class REC

rec(): rec

`rec<-`(): rec<-

accessor(<FEA>): accessor

`accessor<-`(<FEA>): accessor<-

`accessor<-`(<FID>): accessor<-

accessor(<FID>): accessor

accessor(<FNG>): accessor

`accessor<-`(<FNG>): accessor<-

accessor(<FOM>): accessor

`accessor<-`(<FOM>): accessor<-

accessor(<OBS>): accessor

`accessor<-`(<OBS>): accessor<-

accessor(<OID>): accessor

`accessor<-`(<OID>): accessor<-

accessor(<ONG>): accessor

`accessor<-`(<ONG>): accessor<-

analyte(<FOM>): analyte

`analyte<-`(<FOM>): analyte<-

analyte_description(<FOM>): analyte_description

`analyte_description<-`(<FOM>): analyte_description<-

data_type(<FOM>): data_type

`data_type<-`(<FOM>): data_type<-

dataset_id(<FEA>): dataset_id

`dataset_id<-`(<FEA>): dataset_id<-

`dataset_id<-`(<FID>): dataset_id<-

dataset_id(<FID>): dataset_id

dataset_id(<FNG>): dataset_id

`dataset_id<-`(<FNG>): dataset_id<-

dataset_id(<FOM>): dataset_id

`dataset_id<-`(<FOM>): dataset_id<-

dataset_id(<OBS>): dataset_id

`dataset_id<-`(<OBS>): dataset_id<-

dataset_id(<OID>): dataset_id

`dataset_id<-`(<OID>): dataset_id<-

dataset_id(<ONG>): dataset_id

`dataset_id<-`(<ONG>): dataset_id<-

dataset_id(<REC>): dataset_id

`dataset_id<-`(<REC>): dataset_id<-

edge_metric(<FNG>): edge_metric

`edge_metric<-`(<FNG>): edge_metric<-

edge_metric(<ONG>): edge_metric

`edge_metric<-`(<ONG>): edge_metric<-

fea(<MAMS>,<character>,<character>): fea

`fea<-`(<MAMS>,<character>,<character>): fea<-

feature_modality(<FEA>): feature_modality

`feature_modality<-`(<FEA>): feature_modality<-

feature_subset(<FOM>): feature_subset

`feature_subset<-`(<FOM>): feature_subset<-

feature_subset_description(<FOM>): feature_subset_description

representation_description(<FOM>): representation_description

`representation_description<-`(<FOM>): representation_description<-

`feature_subset_description<-`(<FOM>): feature_subset_description<-

fid(<MAMS>,<character>,<character>): fid

`fid<-`(<MAMS>,<character>,<character>): fid<-

filepath(<FEA>): filepath

`filepath<-`(<FEA>): filepath<-

`filepath<-`(<FID>): filepath<-

filepath(<FID>): filepath

filepath(<FNG>): filepath

`filepath<-`(<FNG>): filepath<-

filepath(<FOM>): filepath

`filepath<-`(<FOM>): filepath<-

filepath(<OBS>): filepath

`filepath<-`(<OBS>): filepath<-

filepath(<OID>): filepath

`filepath<-`(<OID>): filepath<-

filepath(<ONG>): filepath

`filepath<-`(<ONG>): filepath<-

fng(<MAMS>,<character>,<character>) `fng<-`(<MAMS>,<character>,<character>): fng

representation(<FOM>): representation

`representation<-`(<FOM>): representation<-

fom(<MAMS>,<character>,<character>): fom

`fom<-`(<MAMS>,<character>,<character>): fom<-

id(<FEA>): id

`id<-`(<FEA>): id<-

`id<-`(<FID>): id<-

id(<FID>): id

id(<FNG>): id

`id<-`(<FNG>): id<-

id(<FOM>): id

`id<-`(<FOM>): id<-

id(<OBS>): id

`id<-`(<OBS>): id<-

id(<OID>): id

`id<-`(<OID>): id<-

id(<ONG>): id

`id<-`(<ONG>): id<-

id(<REC>): id

`id<-`(<REC>): id<-

reference_organism(<FEA>): reference_organism

`reference_organism<-`(<FEA>): reference_organism<-

metric_type(<FNG>): metric_type

`metric_type<-`(<FNG>): metric_type<-

metric_type(<ONG>): metric_type

`metric_type<-`(<ONG>): metric_type<-

modality(<FOM>): modality

`modality<-`(<FOM>): modality<-

obs(<MAMS>,<character>,<character>): obs

`obs<-`(<MAMS>,<character>,<character>): obs<-

obs_subset(<FOM>): obs_subset

`obs_subset<-`(<FOM>): obs_subset<-

obs_subset_description(<FOM>): obs_subset_description

`obs_subset_description<-`(<FOM>): obs_subset_description<-

obs_unit(<FOM>): obs_unit

`obs_unit<-`(<FOM>): obs_unit<-

obs_unit_description(<FOM>) `obs_unit_description<-`(<FOM>): obs_unit_description

oid(<MAMS>,<character>,<character>): oid

`oid<-`(<MAMS>,<character>,<character>): oid<-

ong(<MAMS>,<character>,<character>): ong

`ong<-`(<MAMS>,<character>,<character>): ong<-

reference_database(<FEA>): reference_database

`reference_database<-`(<FEA>): reference_database<-

parent_id(<FNG>): parent_id

`parent_id<-`(<FNG>): parent_id<-

parent_id(<FOM>): parent_id

`parent_id<-`(<FOM>): parent_id<-

parent_id(<ONG>): parent_id

`parent_id<-`(<ONG>): parent_id<-

parent_relationship(<FOM>): parent_relationship

`parent_relationship<-`(<FOM>): parent_relationship<-

parent_relationship_description(<FOM>): parent_relationship_description

`parent_relationship_description<-`(<FOM>): parent_relationship_description<-

processing(<FOM>): processing

`processing<-`(<FOM>): processing<-

processing_description(<FOM>): processing_description

`processing_description<-`(<FOM>): processing_description<-

rec(<MAMS>,<character>,<character>): rec

`rec<-`(<MAMS>,<character>,<character>): rec<-

record_function_name(<REC>): record_function_name

`record_function_name<-`(<REC>): record_function_name<-

record_workflow_link(<REC>): record_workflow_link

`record_workflow_link<-`(<REC>): record_workflow_link<-

record_function_parameters(<REC>): record_function_parameters

`record_function_parameters<-`(<REC>): record_function_parameters<-

record_id(<FEA>): record_id

`record_id<-`(<FEA>): record_id<-

record_id(<FNG>): record_id

`record_id<-`(<FNG>): record_id<-

record_id(<FOM>): record_id

`record_id<-`(<FOM>): record_id<-

record_id(<OBS>): record_id

`record_id<-`(<OBS>): record_id<-

record_id(<ONG>): record_id

`record_id<-`(<ONG>): record_id<-

record_id(<REC>): record_id

`record_id<-`(<REC>): record_id<-

record_package_name(<REC>): record_package_name

`record_package_name<-`(<REC>): record_package_name<-

record_package_version(<REC>): record_package_version

`record_package_version<-`(<REC>): record_package_version<-

record_runtime_start(<REC>): record_runtime_start

`record_runtime_start<-`(<REC>): record_runtime_start<-

record_runtime_duration(<REC>): record_runtime_duration

`record_runtime_duration<-`(<REC>): record_runtime_duration<-

record_runtime_end(<REC>): record_runtime_end

`record_runtime_end<-`(<REC>): record_runtime_end<-