GRN
object as a data frame.getGRNConnections.Rd
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_TFMetadata = FALSE,
include_peakMetadata = FALSE,
include_geneMetadata = FALSE,
include_variancePartitionResults = FALSE
)
Object of class GRN
Character. One of TF_peaks
, peak_genes
, TF_genes
or all.filtered
. Default all.filtered
. The type of connections to retrieve.
Integer (0 or 1). Default 0
. Either 0
or 1
). Here, 0
refers to the real (foreground) while 1
to the background.
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?
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.
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.source
: Source/Origin of the identified connection. Either neighborhood
, TADs
or knownLinks
,
depending on the parameters used when running the function addConnections_peak_gene
peak_gene.bait_OE_ID
: Only present when known links have been provided (see addConnections_peak_gene
). This column denotes the original IDs of the bait and OE coordinates that identified this link.
peak_gene.tad_ID
: Only present when TADs have been provided (see addConnections_peak_gene
). This column denotes the original ID of the TAD ID that identified this link.
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
).
If the peak-gene connection is across chromosomes (as defined by the known links, see addConnections_peak_gene
), the distance is set to NA.
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
# See the Workflow vignette on the GRaNIE website for examples
GRN = loadExampleObject()
#> Downloading GRaNIE example object from https://git.embl.de/grp-zaugg/GRaNIE/-/raw/master/data/GRN.rds
#> Finished successfully. You may explore the example object. Start by typing the object name to the console to see a summaty. Happy GRaNIE'ing!
GRN_con.all.df = getGRNConnections(GRN)