Returns stored connections/links (either TF-peak, peak-genes, TF-genes or the filtered set of connections as produced by filterGRNAndConnectGenes). Additional meta columns (TF, peak and gene metadata) can be added optionally. Note: This function, as all get functions from this package, does NOT return a GRN object.

getGRNConnections(
GRN,
type = "all.filtered",
background = FALSE,
include_TF_gene_correlations = FALSE,
include_variancePartitionResults = FALSE
)

## Arguments

GRN

Object of class GRN

type

Character. One of TF_peaks, peak_genes, TF_genes or all.filtered. Default all.filtered. The type of connections to retrieve.

background

Integer (0 or 1). Default 0. Either 0 or 1). Here, 0 refers to the real (foreground) while 1 to the background.

include_TF_gene_correlations

Logical. TRUE or FALSE. Default FALSE. Should TFs and gene correlations be returned as well? If set to TRUE, they must have been computed beforehand with add_TF_gene_correlation.

Logical. TRUE or FALSE. Default FALSE. Should TF metadata be returned as well?

Logical. TRUE or FALSE. Default FALSE. Should peak metadata be returned as well?

Logical. TRUE or FALSE. Default FALSE. Should gene metadata be returned as well?

include_variancePartitionResults

Logical. TRUE or FALSE. Default FALSE. Should the results from the function add_featureVariation be included? If set to TRUE, they must have been computed beforehand with add_featureVariation; otherwise, an error is thrown.

## Value

A data frame with the requested connections. This function does **NOT** return a GRN object. Depending on the arguments, the data frame that is returned has different columns, which however can be divided into the following classes according to their name:

• TF-related: Starting with TF.:

• TF.name and TF.ID: Name / ID of the TF

• TF.ENSEMBL: Ensembl ID (unique)

• peak-related: Starting with peak.:

• peak.ID: ID (coordinates)

• peak.mean, peak.median, peak.CV: peak mean, median and its coefficient of variation (CV) across all samples

• peak.annotation: Peak annotation as determined by ChIPseeker such as Promoter, 5’ UTR, 3’ UTR, Exon, Intron, Downstream, Intergenic

• peak.nearestGene*: Additional metadata for the nearest gene such as position (chr, start, end, strand), name (name, symbol and ENSEMBL), and distance to the TSS (distanceToTSS)

• peak.GC.perc: GC percentage

• gene-related: Starting with gene.:

• gene.name and gene.ENSEMBL: gene name and Ensembl ID

• gene.type: gene type (such as protein_coding, lincRNA) as retrieved by biomaRt

• gene.mean, gene.median, gene.CV: gene mean, median and its coefficient of variation (CV) across all samples

• TF-peak-related: Starting with TF_peak.:

• TF_peak.r and TF_peak.r_bin: Correlation coefficient of the TF-peak pair and its correlation bin (in bins of width 0.05, such as (-0.55,-0.5] for r = -0.53)

• TF_peak.fdr and TF_peak.fdr_direction: TF-peak FDR and the directionality from which it was derived (see Methods in the paper, pos or neg)

• TF_peak.connectionType: TF-peak connection type. This is by default expression, meaning that expression was used to construct the TF and peak

• peak-gene-related: Starting with peak_gene.:

• peak_gene.distance: Peak-gene distance (usually taken the TSS of the gene as reference unless specified otherwise, see the parameter overlapTypeGene for more information from addConnections_peak_gene)

• peak_gene.r: Correlation coefficient of the peak-gene pair

• peak_gene.p_raw and peak_gene.p_adj: Raw and adjusted p-value of the peak-gene pair

• TF-gene-related: Starting with TF_gene.:

• TF_gene.r: Correlation coefficient of the TF-gene pair

• TF_gene.p_raw: Raw p-value of the TF-gene pair

filterGRNAndConnectGenes

add_featureVariation

add_TF_gene_correlation

## Examples

# See the Workflow vignette on the GRaNIE website for examples