flowWorkspace
Infrastructure for representing and interacting with gated and ungated cytometry data sets.

Package index
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Vignettes
Functions
798
Source code
54
Man pages
122
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flowWorkspace: Infrastructure for representing and interacting with gated and ungated cytometry data sets.
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API

API for flowWorkspace
Infrastructure for representing and interacting with gated and ungated cytometry data sets.

Global functions
.addGate Source code
.addTrans Source code
.cf_flush_meta Source code
.cf_load_meta Source code
.cf_scale_time_channel Source code
.compareFlowData Source code
.compareGatingHierarchy Source code
.compareGatingSet Source code
.computeCV Source code
.computeCV_gh Source code
.convertTrans Source code
.copyNode Source code
.cpp_CloneGatingSet Source code
.cpp_NewGatingSet Source code
.cpp_addGate Source code
.cpp_boolGating Source code
.cpp_combineGatingSet Source code
.cpp_getChildren Source code
.cpp_getCompensation Source code
.cpp_getGate Source code
.cpp_getGateFlag Source code
.cpp_getHiddenFlag Source code
.cpp_getIndices Source code
.cpp_getLogLevel Source code
.cpp_getNegateFlag Source code
.cpp_getNodeID Source code
.cpp_getNodes Source code
.cpp_getParent Source code
.cpp_getPopStats Source code
.cpp_getSamples Source code
.cpp_getSingleCellExpression Source code
.cpp_getSingleCellExpressionByGate Source code
.cpp_getTransformations Source code
.cpp_loadGatingSet Source code
.cpp_plotGh Source code
.cpp_removeNode Source code
.cpp_saveGatingSet Source code
.cpp_setGate Source code
.cpp_setIndices Source code
.cpp_setLogLevel Source code
.cpp_setNodeFlag Source code
.cpp_setNodeName Source code
.cpp_setSample Source code
.cpp_togleErrorFlag Source code
.flowJoTrans Source code
.getAllDescendants Source code
.getDescendants Source code
.getGraph Source code
.getIndiceMat Source code
.getNodeInd Source code
.getNodes_removeHidden Source code
.getPopChnlMapping Source code
.getPopCounts Source code
.getPopStat Source code
.getSplineCoefs Source code
.getTransformations Source code
.gh_pop_set_indices Source code
.graph_handler Source code
.gslist_get_pop_stats Source code
.isCompensated Source code
.layoutGraph Source code
.load_legacy Source code
.matchCols Source code
.mergeGates Source code
.moveNode Source code
.onAttach Source code
.onLoad Source code
.preprocessMap Source code
.renameMarker Source code
.set.count.xml Source code
.updateChannels Source code
.uuid_gen Source code
GatingHierarchy Man page
GatingHierarchy-class Man page
GatingSet Man page
GatingSet,GatingHierarchy,character-method Man page
GatingSet,cytoset,ANY-method Man page
GatingSet,flowSet,ANY-method Man page
GatingSet,flowSet-method Man page
GatingSet-class Man page
GatingSet-methods Man page
GatingSetList Man page Source code
GatingSetList-class Man page
LdFlags Source code
Rm Man page Source code
[ Man page
[,GatingSet,ANY,ANY,ANY-method Man page
[,GatingSet,ANY-method Man page
[,GatingSetList,ANY-method Man page
[,cytoframe,ANY-method Man page
[,cytoset,ANY-method Man page
[[ Man page
[[,GatingSet,character-method Man page
[[,GatingSet,logical-method Man page
[[,GatingSet,numeric-method Man page
[[,cytoset,ANY-method Man page
[[<-,GatingSet,ANY,ANY,GatingHierarchy-method Man page
[[<-,cytoset,ANY,ANY,flowFrame-method Man page
add Man page Source code
add,default-method Man page
add.default Source code
add_cytoframe Source code
append_cols Source code
asinh_Gml2 Man page Source code
asinhtGml2_trans Man page Source code
backend_type Source code
booleanFilter Man page Source code
booleanFilter-class Man page
brackets Man page
cf_append_cols Man page Source code
cf_backend_type Man page Source code
cf_cleanup Man page Source code
cf_cleanup_temp Man page Source code
cf_flush_meta Man page Source code
cf_getData Source code
cf_getKeyword Source code
cf_getKeywords Source code
cf_get_h5_file_path Man page Source code
cf_get_uri Man page Source code
cf_is_indexed Source code
cf_is_subsetted Man page Source code
cf_keyword_delete Man page Source code
cf_keyword_insert Man page Source code
cf_keyword_rename Man page Source code
cf_keyword_set Man page Source code
cf_load_meta Man page Source code
cf_lock Man page Source code
cf_removeKeywords Source code
cf_renameKeywords Source code
cf_rename_channel Man page Source code
cf_rename_marker Man page Source code
cf_scale_time_channel Source code
cf_setData Source code
cf_setKeywords Source code
cf_setKeywordsSubset Source code
cf_set_readonly Source code
cf_swap_colnames Man page Source code
cf_to_memcf Source code
cf_transform_data Source code
cf_unlock Man page Source code
cf_write_disk Man page Source code
cf_write_h5 Man page Source code
cf_write_tile Man page Source code
char2booleanFilter Man page Source code
checkRedundantNodes Man page Source code
check_comp Source code
check_credential Source code
cleanup Man page
cleanup_temp Man page
colnames,GatingHierarchy-method Man page
colnames,GatingSet-method Man page
colnames,cytoframe-method Man page
colnames,cytoset-method Man page
colnames<-,GatingHierarchy-method Man page
colnames<-,GatingSet,ANY-method Man page
colnames<-,GatingSet-method Man page
colnames<-,cytoframe-method Man page
colnames<-,cytoset-method Man page
compensate Man page
compensate,GatingSet,ANY-method Man page
compensate,GatingSetList,ANY-method Man page
compensate,cytoframe,matrix-method Man page
compensate,cytoset,ANY-method Man page
compensate,cytoset,list-method Man page
compensate,cytoset,matrix-method Man page
convert Man page
convert_backend Man page Source code
convert_legacy_gs Man page Source code
convert_legacy_gslist Man page Source code
copyNode Man page Source code
copy_view Source code
copy_view.cytoframe Source code
copy_view.cytoset Source code
copy_view_cytoframe Source code
copy_view_cytoset Source code
cpp_gating Source code
cs_add_cytoframe Man page Source code
cs_cleanup Man page
cs_cleanup_temp Man page Source code
cs_flush_meta Man page Source code
cs_get_cytoframe Man page Source code
cs_get_h5_file_path Man page Source code
cs_get_uri Man page Source code
cs_is_subsetted Man page Source code
cs_keyword_delete Man page Source code
cs_keyword_insert Man page Source code
cs_keyword_rename Man page Source code
cs_keyword_set Man page Source code
cs_load_meta Man page Source code
cs_lock Man page Source code
cs_set_compensation Source code
cs_set_cytoframe Man page Source code
cs_swap_colnames Man page Source code
cs_unlock Man page Source code
cytoframe Man page
cytoframe-class Man page
cytoframe-labels Man page
cytoframe_to_flowFrame Man page Source code
cytoset Man page Source code
cytoset-class Man page
cytoset_to_flowSet Man page Source code
cytoset_to_list Man page Source code
delete_gs Man page Source code
dropRedundantChannels Man page Source code
dropRedundantNodes Man page Source code
estimateLogicle Man page
estimateLogicle,GatingHierarchy-method Man page
estimateLogicle,GatingSet-method Man page
estimateLogicle.GatingHierarchy Man page Source code
extract_cluster_pop_name_from_node Man page Source code
fcs_to_cytoset Source code
filterObject Man page Source code
filterObject,default-method Man page
filterObject.default Source code
filter_to_list Man page Source code
filter_to_list,booleanFilter-method Man page
filter_to_list,ellipsoidGate-method Man page
filter_to_list,logical-method Man page
filter_to_list,polygonGate-method Man page
filter_to_list,quadGate-method Man page
filter_to_list,rectangleGate-method Man page
filter_to_list.booleanFilter Source code
filter_to_list.ellipsoidGate Source code
filter_to_list.logical Source code
filter_to_list.polygonGate Source code
filter_to_list.quadGate Source code
filter_to_list.rectangleGate Source code
fix_y_axis Source code
flowData Man page
flowData,GatingSet-method Man page
flowData<- Man page
flowData<-,GatingSet-method Man page
flowFrame_to_cytoframe Man page Source code
flowJo.fasinh Man page Source code
flowJo.flog Man page Source code
flowJo.fsinh Man page Source code
flowJoTrans Man page Source code
flowJo_biexp_trans Man page Source code
flowJo_fasinh_trans Man page Source code
flowSet_to_cytoset Man page Source code
flowSet_to_list Man page
flowWorkspace Man page
flowWorkspace-deprecated Man page
flowWorkspace-package Man page
flow_breaks Man page Source code
flow_trans Man page Source code
flowjo_biexp Man page Source code
flowjo_biexp_trans Man page Source code
flowjo_fasinh Man page
flowjo_fasinh_trans Man page Source code
flowjo_flog Man page
flowjo_fsinh Man page Source code
flowjo_log_trans Man page Source code
flush_meta Man page
frm_compensate Source code
gen_uid Source code
getChildren Man page
getChildren,GatingSet,character-method Man page
getCompensationMatrices Man page Source code
getCompensationMatrices,GatingHierachy-method Man page
getCompensationMatrices.GatingHierarchy Source code
getData Man page
getData,GatingHierarchy-method Man page
getData,GatingSet-method Man page
getData,GatingSetList-method Man page
getDescendants Man page Source code
getDescendants,GatingHierarchy-method Man page
getGate Man page
getGate,GatingHierarchy,character-method Man page
getGate,GatingSet,character-method Man page
getGate,GatingSetList,character-method Man page
getIndices Man page
getIndices,GatingHierarchy,character-method Man page
getMergedStats Source code
getNodePath Source code
getNodes Man page
getNodes,GatingSet-method Man page
getParent Man page
getParent,GatingSet,character-method Man page
getPopStats Man page
getPopStats,GatingHierarchy-method Man page
getPopStats,GatingSet-method Man page
getProp Man page Source code
getSingleCellExpression Man page Source code
getSingleCellExpressionByGate Man page Source code
getStats Man page Source code
getStats,GatingHierarchy-method Man page
getStats,GatingSet-method Man page
getStats,GatingSetList-method Man page
getStats.GatingHierarchy Source code
getStats.GatingSet Source code
getStats.GatingSetList Source code
getTotal Man page Source code
getTransformations Man page Source code
getTransformations,GatingHierarchy-method Man page
getTransformations.GatingHierarchy Source code
get_colnames Source code
get_cytoframe Source code
get_cytoframe_from_cs Man page
get_cytoset Source code
get_cytoset_from_node Source code
get_default_backend Man page Source code
get_gatingset_id Source code
get_leaf_nodes Man page Source code
get_log_level Man page Source code
get_pheno_data Source code
get_uri Source code
getncol Source code
getnrow Source code
getpdata Source code
gh_apply_to_cs Man page Source code
gh_apply_to_new_fcs Man page Source code
gh_cleanup Man page
gh_cleanup_temp Man page Source code
gh_copy_gate Man page Source code
gh_get_cluster_labels Man page Source code
gh_get_compensations Man page Source code
gh_get_leaf_nodes Man page
gh_get_pop_paths Man page
gh_get_transformations Man page Source code
gh_keyword_delete Man page Source code
gh_keyword_insert Man page Source code
gh_keyword_rename Man page Source code
gh_keyword_set Man page Source code
gh_plot_pop_count_cv Man page Source code
gh_pop_compare_stats Man page Source code
gh_pop_get_children Man page
gh_pop_get_cluster_name Man page Source code
gh_pop_get_count Man page Source code
gh_pop_get_data Man page Source code
gh_pop_get_descendants Man page Source code
gh_pop_get_full_path Man page Source code
gh_pop_get_gate Man page Source code
gh_pop_get_indices Man page Source code
gh_pop_get_indices_mat Man page Source code
gh_pop_get_parent Man page
gh_pop_get_proportion Man page Source code
gh_pop_get_stats Man page Source code
gh_pop_get_stats_tfilter Man page Source code
gh_pop_is_bool_gate Man page Source code
gh_pop_is_gated Man page Source code
gh_pop_is_hidden Man page Source code
gh_pop_is_negated Man page Source code
gh_pop_move Man page Source code
gh_pop_normalize_idx Source code
gh_pop_remove Man page Source code
gh_pop_set_gate Man page Source code
gh_pop_set_indices Man page Source code
gh_pop_set_name Man page Source code
gh_pop_set_visibility Man page Source code
gh_pop_set_xml_count Man page Source code
groupByChannels Man page Source code
groupByTree Man page Source code
gs_check_redundant_nodes Man page Source code
gs_cleanup Man page
gs_cleanup_temp Man page Source code
gs_clone Source code
gs_copy_tree_only Source code
gs_cyto_data Man page
gs_cyto_data,GatingSet-method Man page
gs_cyto_data<- Man page
gs_cyto_data<-,GatingSet-method Man page
gs_get_compensation_internal Man page Source code
gs_get_compensations Man page Source code
gs_get_cytoframe Man page Source code
gs_get_leaf_nodes Man page Source code
gs_get_pop_paths Man page Source code
gs_get_singlecell_expression Man page Source code
gs_get_singlecell_expression_by_gate Man page Source code
gs_get_transformlists Source code
gs_get_uri Man page Source code
gs_is_dirty Source code
gs_is_h5 Man page Source code
gs_is_persistent Man page Source code
gs_keyword_delete Man page Source code
gs_keyword_insert Man page Source code
gs_keyword_rename Man page Source code
gs_keyword_set Man page Source code
gs_plot_diff_tree Man page Source code
gs_plot_pop_count_cv Man page Source code
gs_pop_add Man page Source code
gs_pop_get_children Man page Source code
gs_pop_get_count_fast Man page Source code
gs_pop_get_count_with_meta Man page Source code
gs_pop_get_data Man page Source code
gs_pop_get_gate Man page Source code
gs_pop_get_gs Man page Source code
gs_pop_get_parent Man page Source code
gs_pop_get_stats Man page Source code
gs_pop_get_stats_tfilter Man page Source code
gs_pop_remove Man page Source code
gs_pop_set_gate Man page Source code
gs_pop_set_name Man page Source code
gs_pop_set_visibility Man page Source code
gs_remove_redundant_channels Man page Source code
gs_remove_redundant_nodes Man page Source code
gs_split_by_channels Man page Source code
gs_split_by_tree Man page Source code
gs_transform_data Source code
gs_update_channels Man page Source code
gslist_to_gs Man page Source code
h5_set_error_handler Source code
identifier Man page
identifier,GatingSet-method Man page
identifier,GatingSetList-method Man page
identifier,cytoset-method Man page
identifier-methods Man page
identifier<-,GatingSet,ANY-method Man page
identifier<-,GatingSet,character-method Man page
identifier<-,GatingSet-method Man page
identifier<-,GatingSetList,ANY-method Man page
identifier<-,GatingSetList,character-method Man page
identifier<-,cytoset,ANY-method Man page
isGated Man page Source code
isHidden Man page Source code
isNcdf Man page Source code
isNegated Man page Source code
is_http_path Source code Source code
is_s3_path Source code
is_tiledb_support Man page Source code
keyword Man page
keyword,GatingHierarchy,character-method Man page
keyword,GatingHierarchy,missing-method Man page
keyword,GatingSet,character-method Man page
keyword,GatingSet,missing-method Man page
keyword,GatingSetList,character-method Man page
keyword,GatingSetList,missing-method Man page
keyword,cytoframe,missing-method Man page
keyword-mutators Man page
lapply Man page
lapply,GatingSet-method Man page
lapply,cytoset-method Man page
lapply-methods Man page
length Man page
length,GatingSet-method Man page
load_cf Source code
load_cytoframe Man page Source code
load_cytoframe_from_fcs Man page Source code
load_cytoset Man page Source code
load_cytoset_from_fcs Man page Source code
load_gs Man page Source code
load_gslist Man page Source code
load_legacy_gs Source code
load_meta Man page
lock Man page
logicleGml2_trans Man page
logicle_trans Man page Source code
logtGml2_trans Man page
markernames Man page
markernames,GatingHierarchy-method Man page
markernames,GatingSet-method Man page
markernames,cytoframe-method Man page
markernames,cytoset-method Man page
markernames<-,GatingHierarchy-method Man page
markernames<-,GatingSet,ANY-method Man page
markernames<-,GatingSet-method Man page
markernames<-,cytoframe-method Man page
markernames<-,cytoset-method Man page
markernmaes<-,cytoframe-method Man page
merge-GatingSet Man page
merge_list_to_gs Man page Source code
moveNode Man page Source code
ncFlowSet Man page
ncFlowSet,GatingSet-method Man page
ncFlowSet<- Man page
ncFlowSet<-,GatingSet-method Man page
new_cytoset Source code
nodeflags Man page
openWorkspace Man page Source code
pData Man page
pData,GatingHierarchy-method Man page
pData,GatingSet-method Man page
pData,cytoset-method Man page
pData-methods Man page
pData<- Man page
pData<-,GatingSet,data.frame-method Man page
pData<-,GatingSetList,data.frame-method Man page
pData<-,cytoset,data.frame-method Man page
parseFCS Source code
parse_s3_path Source code
parse_transformer Source code
phenoData,cytoset-method Man page
phenoData<-,cytoset,ANY-method Man page
plot Man page
plot,GatingSet,character-method Man page
plot,GatingSet,missing-method Man page
plot-methods Man page
plotGate Man page
plotGate,GatingHierarchy,character-method Man page
plotGate,GatingHierarchy,missing-method Man page
plotGate,GatingHierarchy,numeric-method Man page
plotGate,GatingSet,character-method Man page
plotGate,GatingSet,missing-method Man page
plotGate,GatingSet,numeric-method Man page
plotGate,GatingSetList,character-method Man page
plotGate-methods Man page
plotGate-methods-defunct Man page
pop.MFI Man page Source code
pop_add Man page Source code
pop_add.factor Man page Source code
pop_add.filter Man page Source code
pop_add.filters Man page Source code
pop_add.logical Man page Source code
pop_add.logicalFilterResult Man page Source code
pop_add.multipleFilterResult Man page Source code
pop_add.quadGate Man page Source code
prettyAxis Man page Source code
process_spill_keyword Source code
rbind2,GatingSetList,missing-method Man page
realize_view Man page Source code
realize_view,cytoframe-method Man page
realize_view,cytoset-method Man page
realize_view.cytoframe Source code
realize_view.cytoset Source code
realize_view_cytoframe Source code
realize_view_cytoset Source code
recompute Man page Source code
recompute.GatingSet Man page Source code
recompute.GatingSetList Man page Source code
rotate_gate Man page
rotate_gate,GatingHierarchy-method Man page
rotate_gate,GatingSet-method Man page
rotate_gate.GatingHierarchy Man page Source code
rotate_gate.GatingSet Source code
sampleNames Man page
sampleNames,GatingSet-method Man page
sampleNames,character-method Man page
sampleNames,cytoset, Man page
sampleNames,cytoset-method Man page
sampleNames<- Man page
sampleNames<-,GatingSet,ANY-method Man page
sampleNames<-,GatingSet-method Man page
sampleNames<-,cytoset,ANY-method Man page
save_cytoset Man page Source code
save_gs Man page Source code
save_gslist Man page Source code
scale_gate Man page
scale_gate,GatingHierarchy-method Man page
scale_gate,GatingSet-method Man page
scale_gate.GatingHierarchy Man page Source code
scale_gate.GatingSet Source code
setChannel Source code
setGate Man page
setGate,GatingHierarchy,character,filter-method Man page
setGate,GatingSet,character,ANY-method Man page
setMarker Source code
setNode Man page
setNode,GatingHierarchy,character,ANY-method Man page
setNode,GatingHierarchy,character,character-method Man page
setNode,GatingHierarchy,character,logical-method Man page
setNode,GatingSet,character,ANY-method Man page
set_all_channels Source code
set_cytoframe Source code
set_cytoset Source code
set_default_backend Man page Source code
set_gatingset_id Source code
set_log_level Man page Source code
set_pheno_data Source code
set_quadgate Source code
set_transformations Source code
setpdata Source code
shift_gate Man page
shift_gate,GatingHierarchy-method Man page
shift_gate,GatingSet-method Man page
shift_gate.GatingHierarchy Man page Source code
shift_gate.GatingSet Source code
show,GatingHierarchy-method Man page
show,GatingSet-method Man page
show,booleanFilter-method Man page
show,cytoset-method Man page
standardize-GatingSet Man page
stats.fun Man page
subset Man page
subset.GatingSet Man page
subset_cytoframe_by_cols Source code
subset_cytoframe_by_rows Source code
subset_cytoset Source code
subset_cytoset_by_rows Source code
subset_gs_by_sample Source code
swap_data_cols Man page Source code
transform Man page
transform,GatingSet-method Man page
transform,GatingSetList-method Man page
transform,cytoset-method Man page
transform_gate Man page
transform_gate,GatingHierarchy-method Man page
transform_gate,GatingSet-method Man page
transform_gate.GatingHierarchy Man page Source code
transform_gate.GatingSet Source code
transformerList Man page
updateChannels Man page Source code
updateIndices Man page
updateIndices,GatingHierarchy,character,logical-method Man page
validGatingSetListObject Source code
validitycheck Source code
write_to_disk Source code
flowWorkspace documentation built on Nov. 8, 2020, 8:08 p.m.

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