sircleORA
sircleORA.RdUses enricher to run ORA on each of the clusters as defined by the regulatory labels using prior knowledge such as gene-sets
Usage
sircleORA(
InputData,
geneID,
regLabels = "RegulatoryLabels",
PriorKnowledge,
PKName = "",
emptyRegLabel = "",
RemoveBackgroundGenes = "TRUE",
Plot_FileType = "pdf",
minGSSize = 10,
maxGSSize = 1000,
Plot_p.adj = 0.2,
Plot_Percentage = 10,
OutputFileName = ""
)Arguments
- InputData
DF with column gene names amd regulatory labels (i.e. sircle clusters). Usually output from SiRCle RCM functions.
- geneID
Provide column name for the gene ID in InputData. Needs to match the the gene ID in the pathway file provided
- regLabels
Optional: Column name of the column with the regulatory labels in InputData. default: "RegulatoryLabels"
- PriorKnowledge
DF including the prior knowledge (PK), ie. pathway file. File must include column "term" with the pathway or TF-regulon name, column "gene" with the gene name and column "Description" with description that will be depicted on the plots.
- PKName
Optional: Name of the prior knowledge used, i.e. pathway name such as KEGG default: ""
- emptyRegLabel
Optional: Column name of the empty regulatory group default: ""
- Plot_FileType
Optional: Output file type for the figures one of: "svg", "pdf", "png" default: "pdf"
- minGSSize
Optional: minimum group size in ORA default: 10
- maxGSSize
Optional: maximum group size in ORA default: 1000
- Plot_p.adj
Optional: q value cutoff from ORA that should be plotted default: 0.2
- Plot_Percentage
Optional: Percentage of genes that are detected of a pathway default: 10
- OutputFileName
Optional: Output filename default: ""
- RemoveBackgroundGenesOptional: If TRUE, genes that fall into background based on the choosen Background method for SiRCle RCM are removed from the universe. default: "TRUE"