Hyper-geometric p-value enrichment analyses, looking for over-representation of a set of genes on given pathways.
HPEA(genes, geneset, background.genes.size)DA gene names to be checked if they are over-represented or not.
Pathways to be used in enrichment analyses. If not set vp2008 (Chaussabel, 2008) immune modules will be used. This can be set to any geneset using `read.gmt` function from `qusage` package. Different modules are available: https://www.gsea-msigdb.org/gsea/downloads.jsp.
number of background genes for hyper-geometric p-value calculations. Default is 20,000.
data.frame, list of pathways and their enrichment (adjusted) p-values.
# \donttest{
library(cinaR)
data("VP2008")
genes.to.test <- vp2008[[1]][1:10]
HPEA(genes.to.test,vp2008, background.genes.size = 20e3)
#> module.name p.val
#> Plasma cells Plasma cells 1.853276e-26
#> Erythrocytes Erythrocytes 1.251584e-04
#> Platelets Platelets 1.000000e+00
#> B cells B cells 1.000000e+00
#> U_cAMP/NF-KB activation U_cAMP/NF-KB activation 1.000000e+00
#> Myeloid lineage 1 Myeloid lineage 1 1.000000e+00
#> U_P53 signaling U_P53 signaling 1.000000e+00
#> MHC/Ribosomal proteins MHC/Ribosomal proteins 1.000000e+00
#> U_metabolism/replication U_metabolism/replication 1.000000e+00
#> Cytotoxic cells Cytotoxic cells 1.000000e+00
#> Neutrophils Neutrophils 1.000000e+00
#> Ribosomal proteins Ribosomal proteins 1.000000e+00
#> U_Immunity/cytoskeleton U_Immunity/cytoskeleton 1.000000e+00
#> Myeloid lineage 2 Myeloid lineage 2 1.000000e+00
#> Unknown Unknown 1.000000e+00
#> T Cells T Cells 1.000000e+00
#> U_T cells/cytoskeleton U_T cells/cytoskeleton 1.000000e+00
#> U_Immsurface/cytokines/signaling U_Immsurface/cytokines/signaling 1.000000e+00
#> U_RAS/kinases U_RAS/kinases 1.000000e+00
#> Interferon-inducible Interferon-inducible 1.000000e+00
#> Inflammation I Inflammation I 1.000000e+00
#> Inflammation II Inflammation II 1.000000e+00
#> U_protphosphatases/PI3K U_protphosphatases/PI3K 1.000000e+00
#> U_hemoglobin U_hemoglobin 1.000000e+00
#> U_mitochondrial proteins U_mitochondrial proteins 1.000000e+00
#> U_proteasome/ubiquitin cx U_proteasome/ubiquitin cx 1.000000e+00
#> U_enzymes U_enzymes 1.000000e+00
#> U_kinases/phosphatases U_kinases/phosphatases 1.000000e+00
#> overlapping.genes
#> Plasma cells IGHD,PLEKHG1,C13orf18,ZDHHC23,HLA-DOA,MS4A1,TCF4,HTPAP,SMC6L1,IGHM
#> Erythrocytes IGHD,IGHM
#> Platelets
#> B cells
#> U_cAMP/NF-KB activation
#> Myeloid lineage 1
#> U_P53 signaling
#> MHC/Ribosomal proteins
#> U_metabolism/replication
#> Cytotoxic cells
#> Neutrophils
#> Ribosomal proteins
#> U_Immunity/cytoskeleton
#> Myeloid lineage 2
#> Unknown
#> T Cells
#> U_T cells/cytoskeleton
#> U_Immsurface/cytokines/signaling
#> U_RAS/kinases
#> Interferon-inducible
#> Inflammation I
#> Inflammation II
#> U_protphosphatases/PI3K
#> U_hemoglobin
#> U_mitochondrial proteins
#> U_proteasome/ubiquitin cx
#> U_enzymes
#> U_kinases/phosphatases
#> module.overlapping.ratio adj.p
#> Plasma cells 0.17241379 5.189173e-25
#> Erythrocytes 0.05882353 1.752218e-03
#> Platelets 0.00000000 1.000000e+00
#> B cells 0.00000000 1.000000e+00
#> U_cAMP/NF-KB activation 0.00000000 1.000000e+00
#> Myeloid lineage 1 0.00000000 1.000000e+00
#> U_P53 signaling 0.00000000 1.000000e+00
#> MHC/Ribosomal proteins 0.00000000 1.000000e+00
#> U_metabolism/replication 0.00000000 1.000000e+00
#> Cytotoxic cells 0.00000000 1.000000e+00
#> Neutrophils 0.00000000 1.000000e+00
#> Ribosomal proteins 0.00000000 1.000000e+00
#> U_Immunity/cytoskeleton 0.00000000 1.000000e+00
#> Myeloid lineage 2 0.00000000 1.000000e+00
#> Unknown 0.00000000 1.000000e+00
#> T Cells 0.00000000 1.000000e+00
#> U_T cells/cytoskeleton 0.00000000 1.000000e+00
#> U_Immsurface/cytokines/signaling 0.00000000 1.000000e+00
#> U_RAS/kinases 0.00000000 1.000000e+00
#> Interferon-inducible 0.00000000 1.000000e+00
#> Inflammation I 0.00000000 1.000000e+00
#> Inflammation II 0.00000000 1.000000e+00
#> U_protphosphatases/PI3K 0.00000000 1.000000e+00
#> U_hemoglobin 0.00000000 1.000000e+00
#> U_mitochondrial proteins 0.00000000 1.000000e+00
#> U_proteasome/ubiquitin cx 0.00000000 1.000000e+00
#> U_enzymes 0.00000000 1.000000e+00
#> U_kinases/phosphatases 0.00000000 1.000000e+00
# }