# Phenotypes Identification Using Mapper from topological data Analysis

## Documentation for package ‘PIUMA’ version 1.8.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

autoClusterMapper | Automatic Clustering of a Mapper Graph by Predicted Geometry (with kNN tie-break)
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.
getClusters | Getter method for the 'clustering' slot of a TDAobj object.
getClusters,PIUMA-getClusters | Getter method for the 'clustering' slot of a TDAobj object.
getClusters-method | Getter method for the 'clustering' slot of a TDAobj object.
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.
getGraph | Getter method for the 'graph' slot of a TDAobj object.
getGraph,PIUMA-getGraph | Getter method for the 'graph' slot of a TDAobj object.
getGraph-method | Getter method for the 'graph' 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.
getMetric,PIUMA-getMetrics | Getter method for the 'metrics' slot under 'graph' of a TDAobj object.
getMetrics | Getter method for the 'metrics' slot under 'graph' of a TDAobj object.
getMetrics-method | Getter method for the 'metrics' slot under 'graph' 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
predict_mapper_class | Predict Mapper Graph Geometry (lightweight)
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.
setGraph | Setter method for the 'graph' slot of a TDAobj object.
setGraph,PIUMA-setGraph | Setter method for the 'graph' slot of a TDAobj object.
setGraph-method | Setter method for the 'graph' 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