Gene set enrichment analyses, runs 'fgsea' package implementation with preset values.
GSEA(genes, geneset)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.
data.frame, list of pathways and their enrichment (adjusted) p-values.
G. Korotkevich, V. Sukhov, A. Sergushichev. Fast gene set enrichment analysis. bioRxiv (2019), doi:10.1101/060012
# \donttest{
library(cinaR)
library(fgsea)
data(examplePathways)
data(exampleRanks)
GSEA(exampleRanks, examplePathways)
#> pathway
#> 1: 1221633_Meiotic_Synapsis
#> 2: 1445146_Translocation_of_Glut4_to_the_Plasma_Membrane
#> 3: 442533_Transcriptional_Regulation_of_Adipocyte_Differentiation_in_3T3-L1_Pre-adipocytes
#> 4: 508751_Circadian_Clock
#> 5: 5334727_Mus_musculus_biological_processes
#> ---
#> 582: 6096057_Adaptive_Immune_System
#> 583: 6096937_Class_I_MHC_mediated_antigen_processing_&_presentation
#> 584: 6096957_ER-Phagosome_pathway
#> 585: 6096958_Antigen_processing-Cross_presentation
#> 586: 912497_Meiotic_Recombination
#> pval padj log2err ES NES size
#> 1: 0.56790123 0.73622813 0.06628422 0.2885754 0.9314811 27
#> 2: 0.67500000 0.82406250 0.05536428 0.2387284 0.8437176 39
#> 3: 0.10765550 0.26254480 0.21140019 -0.3640706 -1.3489029 31
#> 4: 0.80219780 0.88362389 0.05174055 0.2516324 0.7309702 17
#> 5: 0.36538462 0.56051148 0.07977059 0.2469065 1.0516851 106
#> ---
#> 582: 0.70905923 0.83697073 0.05513518 0.2568888 0.8203128 25
#> 583: 0.70905923 0.83697073 0.05513518 0.2568888 0.8203128 25
#> 584: 0.34385965 0.54305045 0.09255289 0.3477495 1.0987062 23
#> 585: 0.70905923 0.83697073 0.05513518 0.2568888 0.8203128 25
#> 586: 0.01173541 0.05372619 0.38073040 0.5722386 1.6947710 18
#> leadingEdge
#> 1: 15270,12189,71846,19357
#> 2: 17918,19341,20336,22628,22627,20619,16579,16568,11651,12315,12314,11465,53413,107371,12313
#> 3: 76199,19014,26896,229003,17977,17978,12537,70208,67381,59024,327987,20602
#> 4: 20893,59027,19883
#> 5: 60406,19361,15270,20893,12189,68240,71846,20018,192191,12567,19891,59027,19357
#> ---
#> 582: 26440,26444,26445,19170,26442,19177,667803,12317,53421,19172,19166,19173,16913,26441
#> 583: 26440,26444,26445,19170,26442,19177,667803,12317,53421,19172,19166,19173,16913,26441
#> 584: 26440,26444,26445,19170,26442,19177,667803,12317,53421,19172,19166,19173,16913,26441
#> 585: 26440,26444,26445,19170,26442,19177,667803,12317,53421,19172,19166,19173,16913,26441
#> 586: 19361,15270,12189,68240,12567,19891
# }