exportBB: exportBB

In aertslab/ScoMAP: ScoMAP: Single-Cell Omics Mapping into spatial Axes using Pseudotemporal ordering

Description

Export links to bigInteract format for visualization in UCSC.

Usage

exportBB(
  RF_links = NULL,
  Cor_links = NULL,
  txdb,
  org.db,
  standardized = TRUE,
  save_path = NULL
)

Arguments

RF_links	Data frames list containing RF scores for each region in each gene as returned by enhancerToGene().
Cor_links	Data frames list containing correlation scores for each region in each gene as returned by enhancerToGene(). If both RF and correlation links are provided, the height of the links will represent the RF importance and the color whether the correlation is positive or negative. If only RF is provided, links will be colored black; and if only correlation links are provided the height of the lnk will indicate the absolute correlation value and the color whether it is positive or negative.
txdb	Txdb object matching with the genome assembly used for the analysis
org.db	Org.Db objet for the corresponding species
standardized	Whether link scores (RF or correlation based) should be standardized per gene. This is recommended for visualization in UCSC, as scores must be between 0-1000. Default=TRUE.
save_path	Path to save bb file.
annot	Annotation data frame, as required by cicero (Pliner et al., 2019)

Value

A dataframe containing links in bigInteract format. For more information, please visit https://genome.ucsc.edu/goldenPath/help/interact.html. Scores values will depend on whether RF links and or correlation links are provided, if both are provided RF importances will be used for the score and correlations will be used for the color.

Examples

exportBB(RF_links, Cor_links)

aertslab/ScoMAP documentation built on Oct. 8, 2021, 1:15 a.m.