Gene set enrichment analyses, runs 'fgsea' package implementation with preset values.
Arguments
- genes
DA gene names to be checked if they are over-represented or not.
- geneset
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.
References
G. Korotkevich, V. Sukhov, A. Sergushichev. Fast gene set enrichment analysis. bioRxiv (2019), doi:10.1101/060012
Examples
# \donttest{
library(cinaR)
library(fgsea)
data(examplePathways)
data(exampleRanks)
GSEA(exampleRanks, examplePathways)
#> pathway
#> <char>
#> 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
#> <num> <num> <num> <num> <num> <int>
#> 1: 0.5539305 0.73273881 0.06928365 0.2885754 0.9418916 27
#> 2: 0.6684211 0.81944506 0.05822162 0.2387284 0.8590286 39
#> 3: 0.1192661 0.28410532 0.19578900 -0.3640706 -1.3024359 31
#> 4: 0.8044280 0.90478855 0.05195125 0.2516324 0.7391437 17
#> 5: 0.3813953 0.58694683 0.07998588 0.2469065 1.0453809 106
#> ---
#> 582: 0.7088608 0.84142305 0.05688642 0.2568888 0.8256794 25
#> 583: 0.7088608 0.84142305 0.05688642 0.2568888 0.8256794 25
#> 584: 0.3613139 0.56986701 0.09196861 0.3477495 1.1006039 23
#> 585: 0.7088608 0.84142305 0.05688642 0.2568888 0.8256794 25
#> 586: 0.0248887 0.09349217 0.35248786 0.5722386 1.7116914 18
#> leadingEdge
#> <char>
#> 1: 15270,12189,71846
#> 2: 17918,19341,20336,22628,22627,20619,16579,16568,11651,12315
#> 3: 76199,19014,26896,229003,17977,17978,12537,70208,67381,59024,327987,20602
#> 4: 20893,59027
#> 5: 60406,19361,15270,20893,12189,68240,71846,20018,192191,12567,19891,59027
#> ---
#> 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
# }