| checkNetEntropy |
Compute the Network Entropy |
| checkScaleFreeModel |
Assessment of Scale-Free model fitting |
| dfToDistance |
Compute the Distance Matrix from TDAobj |
| dfToProjection |
Data projection using a Dimensionality Reduction Method |
| df_test_proj |
A dataset to test the 'dfToProjection' and 'dfToDistance' funtions of 'PIUMA' package. |
| getComp |
Getter method for the 'comp' slot of a TDAobj object. |
| getComp,PIUMA-getComp |
Getter method for the 'comp' slot of a TDAobj object. |
| getComp-method |
Getter method for the 'comp' slot of a TDAobj object. |
| getDfMapper |
Getter method for the 'dfMapper' slot of a TDAobj object. |
| getDfMapper,PIUMA-getDfMapper |
Getter method for the 'dfMapper' slot of a TDAobj object. |
| getDfMapper-method |
Getter method for the 'dfMapper' slot of a TDAobj object. |
| getDistMat |
Getter method for the 'dist_mat' slot of a TDAobj object. |
| getDistMat,PIUMA-getDistMat |
Getter method for the 'dist_mat' slot of a TDAobj object. |
| getDistMat-method |
Getter method for the 'dist_mat' slot of a TDAobj object. |
| getJacc |
Getter method for the 'jacc' slot of a TDAobj object. |
| getJacc,PIUMA-getJacc |
Getter method for the 'jacc' slot of a TDAobj object. |
| getJacc-method |
Getter method for the 'jacc' slot of a TDAobj object. |
| getNodeDataMat |
Getter method for the 'node_data_mat' slot of a TDAobj object. |
| getNodeDataMat,PIUMA-getNodeDataMat |
Getter method for the 'node_data_mat' slot of a TDAobj object. |
| getNodeDataMat-method |
Getter method for the 'node_data_mat' slot of a TDAobj object. |
| getOrigData |
Getter method for the 'orig_data' slot of a TDAobj object. |
| getOrigData,PIUMA-getOrigData |
Getter method for the 'orig_data' slot of a TDAobj object. |
| getOrigData-method |
Getter method for the 'orig_data' slot of a TDAobj object. |
| getOutcome |
Getter method for the 'outcome' slot of a TDAobj object. |
| getOutcome,PIUMA-getOutcome |
Getter method for the 'outcome' slot of a TDAobj object. |
| getOutcome-method |
Getter method for the 'outcome' slot of a TDAobj object. |
| getOutcomeFact |
Getter method for the 'outcomeFact' slot of a TDAobj object. |
| getOutcomeFact,PIUMA-getOutcomeFact |
Getter method for the 'outcomeFact' slot of a TDAobj object. |
| getOutcomeFact-method |
Getter method for the 'outcomeFact' slot of a TDAobj object. |
| getScaledData |
Getter method for the 'scaled_data' slot of a TDAobj object. |
| getScaledData,PIUMA-getScaledData |
Getter method for the 'scaled_data' slot of a TDAobj object. |
| getScaledData-method |
Getter method for the 'scaled_data' slot of a TDAobj object. |
| jaccardMatrix |
Compute the Matrix of Jaccard Indexes |
| makeTDAobj |
Import data and generate the TDAobj object |
| makeTDAobjFromSE |
Import SummarizedExperiment data and generate the TDAobj object |
| mapperCore |
Implement the TDA Mapper algorithm on TDAobj |
| PIUMA |
PIUMA: Phenotypes Identification Using Mapper from topological data Analysis |
| setComp |
Setter method for the 'comp' slot of a TDAobj object. |
| setComp,PIUMA-setComp |
Setter method for the 'comp' slot of a TDAobj object. |
| setComp-method |
Setter method for the 'comp' slot of a TDAobj object. |
| setDfMapper |
Setter method for the 'dfMapper' slot of a TDAobj object. |
| setDfMapper,PIUMA-setDfMapper |
Setter method for the 'dfMapper' slot of a TDAobj object. |
| setDfMapper-method |
Setter method for the 'dfMapper' slot of a TDAobj object. |
| setDistMat |
Setter method for the 'dist_mat' slot of a TDAobj object. |
| setDistMat,PIUMA-setDistMat |
Setter method for the 'dist_mat' slot of a TDAobj object. |
| setDistMat-method |
Setter method for the 'dist_mat' slot of a TDAobj object. |
| setJacc |
Setter method for the 'jacc' slot of a TDAobj object. |
| setJacc,PIUMA-setJacc |
Setter method for the 'jacc' slot of a TDAobj object. |
| setJacc-method |
Setter method for the 'jacc' slot of a TDAobj object. |
| setNodeDataMat |
Setter method for the 'node_data_mat' slot of a TDAobj object. |
| setNodeDataMat,PIUMA-setNodeDataMat |
Setter method for the 'node_data_mat' slot of a TDAobj object. |
| setNodeDataMat-method |
Setter method for the 'node_data_mat' slot of a TDAobj object. |
| setOrigData |
Setter method for the 'orig_data' slot of a TDAobj object. |
| setOrigData,PIUMA-setOrigData |
Setter method for the 'orig_data' slot of a TDAobj object. |
| setOrigData-method |
Setter method for the 'orig_data' slot of a TDAobj object. |
| setOutcome |
Setter method for the 'outcome' slot of a TDAobj object. |
| setOutcome,PIUMA-setOutcome |
Setter method for the 'outcome' slot of a TDAobj object. |
| setOutcome-method |
Setter method for the 'outcome' slot of a TDAobj object. |
| setOutcomeFact |
Setter method for the 'outcomeFact' slot of a TDAobj object. |
| setOutcomeFact,PIUMA-setOutcomeFact |
Setter method for the 'outcomeFact' slot of a TDAobj object. |
| setOutcomeFact-method |
Setter method for the 'outcomeFact' slot of a TDAobj object. |
| setScaledData |
Setter method for the 'scaled_data' slot of a TDAobj object. |
| setScaledData,PIUMA-setScaledData |
Setter method for the 'scaled_data' slot of a TDAobj object. |
| setScaledData-method |
Setter method for the 'scaled_data' slot of a TDAobj object. |
| tdaDfEnrichment |
Add information to TDAobj |
| TDAobj-class |
The object 'TDAobj' |
| tda_test_data |
A TDAobj to test the 'PIUMA' package. |
| vascEC_meta |
Example datasets for PIUMA package |
| vascEC_norm |
We tested PIUMA on a subset of the single-cell RNA Sequencing dataset (GSE:GSE193346 generated and published by Feng et al. (2022) on Nature Communication to demonstrate that distinct transcriptional profiles are present in specific cell types of each heart chambers, which were attributed to have roles in cardiac development. In this tutorial, our aim will be to exploit PIUMA for identifying sub-population of vascular endothelial cells, which can be associated with specific heart developmental stages. The original dataset consisted of three layers of heterogeneity: cell type, stage and zone (i.e., heart chamber). Our testing dataset was obtained by subsetting vascular endothelial cells (cell type) by Seurat object, extracting raw counts and metadata. Thus, we filtered low expressed genes and normalized data by DaMiRseq |
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)