2026-16-06
The PEIMAN2 package provides functions and a mined UniProt-based database for singular enrichment analysis (SEA) and protein set enrichment analysis (PSEA) using lists of proteins..
PEIMAN2 includes a bundled internal database so that the package works immediately after installation and remains suitable for CRAN examples and checks. However, the PEIMAN database and UniProt PTM list are updated over time. Users who want the most recent external data can download and cache updated versions directly from the PEIMAN2 database repository here or update their local database manually by following steps in Database Updates section in this readme file.
You can install the released version of PEIMAN from CRAN here with:
install.packages("PEIMAN2")And the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("jafarilab/PEIMAN2")
# or
devtools::install_github("pnickchi/PEIMAN2")By default, PEIMAN2 uses the bundled database included with the installed package version:
enrich1 <- runEnrichment(
protein = exmplData1$pl1,
os.name = "Homo sapiens (Human)"
)To download and cache the latest available external PEIMAN database and UniProt PTM list, use:
update_peiman_database()After updating the cache, you can run enrichment analysis with the latest cached database:
enrich_latest <- runEnrichment(
protein = exmplData1$pl1,
os.name = "Homo sapiens (Human)",
database_version = "latest"
)You can also download and use a specific database version for reproducible analysis:
update_peiman_database(version = "2026-06-15")
enrich_2026_06_15 <- runEnrichment(
protein = exmplData1$pl1,
os.name = "Homo sapiens (Human)",
database_version = "2026-06-15"
)For mass spectrometry translation functions, the UniProt PTM list version can also be selected. For example:
MS_latest <- sea2mass(
x = enrich_latest,
sig.level = 0.05,
ptmlist_version = "latest"
)or with a specific cached PTM list version:
MS_2026_06_15 <- sea2mass(
x = enrich_2026_06_15,
sig.level = 0.05,
ptmlist_version = "2026-06-15"
)The downloaded files are stored in the user's local PEIMAN2 cache directory:
tools::R_user_dir("PEIMAN2", which = "cache")The default value is database_version = "bundled", which uses the internal
database included in the version of the package installed from CRAN. This means
that package loading, examples, and standard workflows do not require internet
access.
# Load PEIMAN2 package
library(PEIMAN2)
# First example dataset
pl1 <- exmplData1$pl1
# Run SEA on the list
enrich1 <- runEnrichment(protein = pl1, os.name = 'Homo sapiens (Human)')
head(enrich1, n = 6)## PTM FreqinPopulation FreqinSample Sample
## 1 N6-(pyridoxal phosphate)lysine 53 5 97
## 2 Isoglutamyl cysteine thioester (Cys-Gln) 7 2 97
## 3 Glycoprotein 4726 41 97
## 4 Thioester bond 11 2 97
## 5 S-cysteinyl cysteine 3 1 97
## 6 Disulfide bond 3885 33 97
## Population pvalue corrected pvalue
## 1 20431 2e-07 7e-06
## 2 20431 4e-06 7e-05
## 3 20431 8e-06 1e-04
## 4 20431 2e-05 2e-04
## 5 20431 7e-05 5e-04
## 6 20431 1e-04 9e-04
## AC
## 1 Q96QU6; Q4AC99; Q8N5Z0; Q8NHS2; P17174
## 2 P01023; A8K2U0
## 3 P08195; P08908; P28222; P28221; P28566; P30939; P28223; P41595; P28335; P46098; O95264; Q70Z44; A5X5Y0; Q13639; P47898; P34969; P21589; P02763; P19652; P20848; P01009; P04217; P08697; P02750; P01023; A8K2U0; U3KPV4; Q9NPC4; Q9UNA3; P05067; P30542; P29274; P29275; P0DMS8; P22760; Q15758; P01011; P54619; Q9UGJ0; Q9UGI9; Q13131
## 4 P01023; A8K2U0
## 5 P01009
## 6 P08195; P08908; P28222; P28221; P28566; P30939; P28223; P41595; P28335; P46098; O95264; Q8WXA8; A5X5Y0; Q13639; P47898; P50406; P34969; P21589; P05408; P02763; P19652; P04217; P08697; P02750; P01023; A8K2U0; P05067; P30542; P29274; P29275; P0DMS8; Q9NS82; P22760
# Second example dataset
pl2 <- exmplData1$pl2
# Run SEA on the list
enrich2 <- runEnrichment(protein = pl2, os.name = 'Homo sapiens (Human)')plotEnrichment(x = enrich1, sig.level = 0.05)## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## ℹ The deprecated feature was likely used in the PEIMAN2 package.
## Please report the issue to the authors.
## This warning is displayed once per session.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
plotEnrichment(x = enrich1, y = enrich2, sig.level = 0.05)
psea_res <- runPSEA(protein = exmplData2, os.name = 'Rattus norvegicus (Rat)', nperm = 100)## Warning: `rerun()` was deprecated in purrr 1.0.0.
## ℹ Please use `map()` instead.
## # Previously
## rerun(100, psea(x = protein, y = pro.pathway, p = pexponent, perm = TRUE))
##
## # Now
## map(1:100, ~ psea(x = protein, y = pro.pathway, p = pexponent, perm = TRUE))
## ℹ The deprecated feature was likely used in the PEIMAN2 package.
## Please report the issue to the authors.
## This warning is displayed once per session.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
head(psea_res[[1]], n = 6)## PTM pval pvaladj FreqinPopulation FreqinSample
## 1 Acetylation 0 0 1787 125
## 2 ADP-ribosylglycine 0 0 4 4
## 3 Cysteine sulfinic acid (-SO2H) 0 0 1 1
## 4 L-cysteine coenzyme A disulfide 0 0 1 1
## 5 N-acetylaspartate 0 0 1 1
## 6 N-acetylglutamate 0 0 1 1
## ES NES nMoreExtreme size Enrichment
## 1 0.7455919 1.177273 3 125 Over presented
## 2 0.7707317 1.470956 29 4 Over presented
## 3 0.9423077 -27.960452 5 1 Under presented
## 4 -0.5817308 34.084507 43 1 Over presented
## 5 -0.9615385 -187.037037 6 1 Under presented
## 6 -0.9663462 25.632576 1 1 Over presented
## AC
## 1 P0C1X8; P11030; P60711; P63259; Q63028; Q62847; Q62848; Q9WUC4; P31399; P29419; P21571; P15999; D3ZAF6; Q9JJW3; O08839; P0DP29; P0DP30; P0DP31; P18418; P26772; P63039; B0K020; P08081; P08082; P45592; Q91ZN1; P11240; Q63768; P10715; P62898; Q9JHL4; Q7M0E3; P62628; Q07266; P84060; P62870; P15429; P07323; P60841; P56571; B0BN94; P55053; P55051; P07483; Q62658; Q32PX7; Q99PF5; Q5XI73; Q63228; P62994; P01946; P02091; P11517; P62959; P82995; P34058; P27321; Q5XI72; P50411; Q6AXU6; Q5BK20; P11980; Q99MZ8; Q792I0; Q66HF9; P15205; Q5M7W5; P30009; P02688; B0BN72; P30904; O35763; P62775; Q05982; Q71UE8; Q9JJ19; P13084; Q01205; P08461; Q920Q0; O88767; P04785; P31044; O55012; P10111; Q6J4I0; Q9R063; Q9EPC6; P02625; Q63475; P51583; Q68A21; P02401; P62982; P62859; Q6RJR6; Q9JK11; Q63945; B0BN85; P07632; Q66HL2; P28042; O35814; P13668; P37377; Q62880; P19332; P68370; Q6P9V9; Q6AYZ1; Q68FR8; Q5XIF6; Q6PEC1; P11232; P62076; P62078; Q9WV97; P48500; P04692; P58775; Q63610; P09495; Q7M767; Q9Z1A5; P63045
## 2 P62986; P62982; P0CG51; Q63429
## 3 O88767
## 4 Q05982
## 5 P60711
## 6 P63259
## leadingEdge
## 1 P62628; P31044; P37377; P45592; P11030; P02625; P29419; P62775; P21571; O88767; P31399; P02688; P08082; P62898; P63045; P62076; P11232; O35814; Q9WUC4; Q62658; Q63228; P07632; Q5XI73; B0K020; P08081; P62959
## 2 P62982; P0CG51; P62986; Q63429
## 3 O88767
## 4 P31044
## 5 P31044
## 6 P31044
plotPSEA(x = psea_res)
plotRunningScore(x = psea_res, nplot = 8) 
psea2mass(x = psea_res, sig.level = 0.05)## MOD_ID name
## 1 MOD:00064 N6-acetyl-L-lysine
## 2 MOD:01819 N6-succinyl-L-lysine
## 3 MOD:00085 N6-methyl-L-lysine
## 4 MOD:00322 1'-methyl-L-histidine
## 5 MOD:00720 L-methionine (R)-sulfoxide
## 6 MOD:00053 N-acetyl-L-glutamic acid
## 7 MOD:00267 L-cysteine sulfinic acid
## def
## 1 "converts an L-lysine residue to N6-acetyl-L-lysine." [ChEBI:17752, DeltaMass:214, OMSSA:24, PubMed:11369851, PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:15350136, PubMed:1680872, PubMed:670159, RESID:AA0055, Unimod:1#K]
## 2 "converts an L-lysine residue to N6-succinyl-L-lysine." [PubMed:16582421, PubMed:21151122, RESID:AA0545]
## 3 "converts an L-lysine residue to N6-methyl-L-lysine." [ChEBI:17604, DeltaMass:165, PubMed:11875433, PubMed:3926756, RESID:AA0076, Unimod:34#K]
## 4 "converts an L-histidine residue to tele-methyl-L-histidine." [PubMed:10601317, PubMed:11474090, PubMed:11875433, PubMed:6692818, PubMed:8076, PubMed:8645219, RESID:AA0317]
## 5 "oxygenates an L-methionine residue to L-methionine sulfoxide R-diastereomer." [ChEBI:45764, PubMed:21406390, PubMed:22116028, PubMed:23911929, RESID:AA0581]
## 6 "converts an L-glutamic acid residue to N-acetyl-L-glutamic acid." [ChEBI:17533, PubMed:6725286, RESID:AA0044]
## 7 "dioxygenates an L-cysteine residue to L-cysteine sulfinic acid." [ChEBI:16345, OMSSA:162, PubMed:12686488, PubMed:9252331, PubMed:9586994, RESID:AA0262, Unimod:425#C]
## FreqinSample
## 1 75
## 2 31
## 3 9
## 4 2
## 5 2
## 6 1
## 7 1