Function reference • ingres

All functions

cellGenesHeatmap(): Plot a cell heatmap

cellPbnPlot(): Plot a cell PBN

clusterGenesHeatmap(): Plot a cluster heatmap

clusterPbnPlot(): Plot a cluster PBN

computePbnByCluster() computePbnBySingleCell(): Compute a Probabilistic Boolean Network (PBN) for each cluster or each cell

createExampleIngresObject() createExampleIngresObjectWithViper(): Create a toy ingres object to use in examples and tests.

createIngresObject(): Create a new ingres object.

createIngresObjectFromSeurat(): Create a new ingres object using the expression data in a Seurat object.

createNetworkGenesTemplate(): Create a network genes data frame. Optionally store it as csv and open it for editing To create an ingres object, a data frame with the network nodes and the corresponding gene symbols must be provided. This function simplifies the process. If the gene nodes are correct gene symbols, then modification is not needed and the returned data frame can be directly passed to the ingres constructors.

getClusterPbns(): Get the cluster PBNs from an ingres object

getExpressionMatrix(): Get the Expression Matrix from an ingres object

getIdents(): Get the idents from an ingres object

getNetwork(): Get the network from an ingres object

getNetworkGenes(): Get the network genes from an ingres object

getSingleCellPbns(): Get the single-cell PBNs from an ingres object

getViperResults(): Get the viper results from an ingres object

ginmlToGraphml(): Convert a GinSim file into a GraphML file GinSim files have the extension .zginml. This utility function converts such files into the GraphML format. keeping the kind - fate, input or gene -, the edge sign and the rule - formulae - data.

graphmlAsTidy(): Convert GraphML format to tidygraph

ingres-class ingres ingresClass ingresObject: The ingres class.

network: An example network, in the format required by the package. The network is a modified version of the one in Remy et al. Cancer Res 75, 4042–4052 (2015)

network_genes: An example dataframe with the genes contained in the network, in the format required by the package

performViper(): Perform VIPER

plotSelectedCell(): Plot the PBN of a cell selected in an interactive plot.

printAllNodes(): Print all nodes in a network For testing and checks purposes.

produceBoolnetNetwork(): Convert an ingres network into a BoolNet one

produceNetworkForCell(): Produce a tidygraph network for a given cell

produceNetworkForCluster(): Produce a tidygraph network for a given cluster

small_blca_wang: An example small Seurat object, using dataset GSE130001 from Wang et al. Genome Med. 2020 Dec;12(1):24.

viper_results: The results of running performViper() on an ingres object created with small_blca_wang, intended to speed up vignettes and examples. This data frame was subset to only contain the genes in the network_genes file, so to keep the file size small.