Help for package pQTLdata

Title:

A Collection of Proteome Panels and Metadata

Version:

0.7

Date:

2026-10-9

Description:

It aggregates protein panel data and metadata for protein quantitative trait locus (pQTL) analysis using 'pQTLtools' (https://jinghuazhao.github.io/pQTLtools/). The package includes data from affinity-based panels such as 'Olink' (https://olink.com/) and 'SomaScan' (https://somalogic.com/), as well as mass spectrometry-based panels from 'CellCarta' (https://cellcarta.com/), 'Seer' (https://seer.bio/) and 'SWATH-MS' (<doi:10.15252/msb.20178126>). The metadata encompasses updated annotations and publication details.

License:

MIT + file LICENSE

URL:

https://jinghuazhao.github.io/pQTLdata/, https://github.com/jinghuazhao/pQTLdata

BugReports:

https://github.com/jinghuazhao/pQTLdata/issues

Depends:

R (≥ 3.5.0)

Imports:

knitr, Rdpack

RdMacros:

Rdpack

Suggests:

bookdown, dplyr, grid, Cairo, EnsDb.Hsapiens.v75, ensembldb, IRanges, org.Hs.eg.db, S4Vectors, VennDiagram

VignetteBuilder:

knitr

LazyData:

Yes

LazyLoad:

Yes

LazyDataCompression:

NeedsCompilation:

Encoding:

UTF-8

Config/roxygen2/version:

8.0.0

Packaged:

2026-10-09 14:31:08 UTC; jhz22

Author:

Jing Hua Zhao

[aut, cre] (0000-0003-4930-3582), Uwe Ligges [ctb], Benjamin Altmann [ctb], Brian Ripley [ctb]

Maintainer:

Jing Hua Zhao <jinghuazhao@hotmail.com>

Repository:

CRAN

Date/Publication:

2026-10-09 15:20:02 UTC

A summary of datasets

Description

It aggregates protein panel data and metadata for protein quantitative trait locus (pQTL) analysis using 'pQTLtools' (https://jinghuazhao.github.io/pQTLtools/). The package includes data from affinity-based panels such as 'Olink' (https://olink.com/) and 'SomaScan' (https://somalogic.com/), as well as mass spectrometry-based panels from 'CellCarta' (https://cellcarta.com/), 'Seer' (https://seer.bio/) and 'SWATH-MS' (doi:10.15252/msb.20178126). The metadata encompasses updated annotations and publication details.

Details

Available data are listed in the following table.

Objects	Description
Datasets
`caprion`	Caprion panel
`inf1`	Olink/INF panel
`Olink_Explore_1536`	Olink/NGS 1472 panels
`Olink_Explore_3072`	Olink/Explore 3072 panels
`Olink_Explore_HT`	Olink/Explore HT panels
`Olink_Target_96`	Olink/Target 96 panels
`Olink_qPCR`	Olink/qPCR panels
`SomaScan160410`	SomaScan panel
`SomaScanV4.1`	SomaScan v4.1 panel
`SomaScan11k`	SomaScan 11k panel
`scallop_inf1`	SCALLOP/INF meta-analysis results
`seer1980`	ST1 from Suhre et al. (2024)
`swath_ms`	A curated SWATH-MS panel, see Ludwig et al. (2018)
Installations
EndNote/	Proteogenomics references
Olink/	Olink-COVID analysis by MGH

Some generic description for the datasets are as follows.

chr Chromosome.
start Start position.
end End position.
gene Gene name.
UniProt UniProt ID.

Usage

Vignettes on package usage:

An Overview of pQTLdata. vignette("pQTLdata").

Author(s)

Jing Hua Zhao in collaboration with other colleagues.

References

Ludwig C, Gillet L, Rosenberger G, Amon S, Collins BC, Aebersold R (2018). “Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial.” Molecular Systems Biology, 14(8), e8126. doi:10.15252/msb.20178126.

Suhre K, Chen Q, Halama A, Mendez K, Dahlin A, Stephan N, Thareja G, Sarwath H, Guturu H, Dwaraka VB, Batzoglou S, Schmidt F, Lasky-Su JA (2024). “A genome-wide association study of mass spectrometry proteomics using the Seer Proteograph platform.” BioRxiv. doi:10.1101/2024.05.27.596028.

Examples


# Olink-SomaScan panel overlap
p <- list(setdiff(inf1$uniprot,"P23560"),
          setdiff(SomaScan160410$UniProt[!is.na(SomaScan160410$UniProt)],"P23560"))
cnames <- c("INF1","SomaScan")
os <- VennDiagram::venn.diagram(x = p, category.names=cnames, filename=NULL,
                                disable.logging = TRUE,height=8,width=8,units="in")
grid::grid.newpage()
grid::grid.draw(os)
m <- merge(inf1,SomaScan160410,by.x="uniprot",by.y="UniProt")
u <- setdiff(with(m,unique(uniprot)),"P23560")
o <- subset(inf1,uniprot %in% u)
dim(o)
vars <- c("UniProt","chr","start","end","extGene","Target","TargetFullName")
s <- subset(SomaScan160410[vars], UniProt %in% u)
dim(s)
us <- s[!duplicated(s),]
dim(us)
us

Olink/Explore 1536 panel

Description

Information based on pilot studies

Usage

data(Olink_Explore_1536)

Format

A data frame with 1,472 rows and 3 variables:

UniProt: UniProt id
Assay: Experimental assay
Panel: Olink panel

Details

Curated from R.

Olink/Explore 3072 panels

Description

Information on all qPCR panels

Usage

data(Olink_Explore_3072)

Format

A data frame with 2,945 rows and 4 variables:

UniProt.ID: UniProt id
Protein.name: Protein name
Gene.name: Gene name
Explore.384.panel: Explore 384 panel

Details

Curated from Excel.

Olink/Explore HT panels

Description

Information on all qPCR panels

Usage

data(Olink_Explore_HT)

Format

A data frame with 5,416 rows and 4 variables:

Olink.ID: Olink id
UniProt.ID: UniProt id
Protein.name: Protein name
Gene.name: Gene name

Details

Curated from Excel.

Olink/Target 96 panels

Description

Information on all Target 96 panels. Individual panels are also available from the companion xlsx in the Olink/ directory.

Usage

data(Olink_Target_96)

Format

A data frame with 1,116 rows and 3 variables:

UniProt: UniProt id
Protein: Protein
Panel: Panel

Details

Curated from Excel.

Olink/qPCR panels

Description

Information on all qPCR panels

Usage

data(Olink_qPCR)

Format

A data frame with 1,112 rows and 7 variables:

UniProt: UniProt id
Panel: Panels
Target: Protein
gene: HGNC symbol
chr: Chromosome
start: start
end: end

Details

Curated from Excel.

SomaScan 11k

Description

This is also the latest panel

Usage

data(SomaScan11k)

Format

A data frame with 10,776 rows and 5 variables:

Sequence.ID: Sequence ID
Full.Name: Full name
Target.Name: Target name
UniProt.ID: UniProt ID
Entrez.Gene.Name: Entrez gene name

Details

curated from SomaLogic website.

Source

https://somalogic.com/somascan-11k-assay/

Somascan panel

Description

This is based on panel used in Sun et al. (2018).

Usage

data(SomaScan160410)

Format

A data frame with 5,178 rows and 10 variables:

SOMAMER_ID: Somamer id
UniProt: UniProt id
Target: Protein target
TargetFullName: Protein target full name
chr: chromosome (1-22,X,Y)
start: start
end: end
entGene: entrez gene
ensGene: ENSEMBL gene
extGene: external gene

Details

from the INTERVAL study.

References

Sun BB, Maranville JC, Peters JE, Stacey D, Staley JR, Blackshaw J, Burgess S, Jiang T, Paige E, Surendran P, Oliver-Williams C, Kamat MA, Prins BP, Wilcox SK, Zimmerman ES, Chi A, Bansal N, Spain SL, Wood AM, Morrell NW, Bradley JR, Janjic N, Roberts DJ, Ouwehand WH, Todd JA, Soranzo N, Suhre K, Paul DS, Fox CS, Plenge RM, Danesh J, Runz H, Butterworth AS (2018). “Genomic atlas of the human plasma proteome.” Nature, 558(7708), 73-79. ISSN 1476-4687 (Electronic) 0028-0836 (Linking). doi:10.1038/s41586-018-0175-2.

SomaScan v4.1

Description

This is the 7k panel

Usage

data(SomaScanV4.1)

Format

A data frame with 7,288 rows and 6 variables:

#: A serial number
SeqID: SeqID
Human.Target.or.Analyte: Human target/analyte
UniProt.ID: UniProt id
GeneID: HGNC symbol
Type: "Protein"

Details

obtained directly from SomaLogic.

Caprion panel

Description

Information based on Caprion pilot studies

Usage

data(caprion)

Format

A data frame with 987 rows and 19 variables:

Gene: HGNC symbols, simplified in four instances
Gene.orig: Original HGNC symbol
Protein: Protein name as recorded in the original Caprion annotation
Accession: Original UniProt accession, retained for compatibility
Protein.Description: Detailed protein information
GO.Cellular.Component: Gene Ontology cellular component annotation
GO.Function: Gene Ontology molecular function annotation
GO.Process: Gene Ontology biological process annotation
ensGenes: Ensembl gene identifiers
chrom: Chromosome annotation
starts: Start positions
ends: End positions
chr: Chromosome annotation
start: Minimum start position
end: Maximum end position
Accession.original: Original UniProt accession, explicitly preserved
Accession.current: Current UniProt accession where resolved; NA for the demerged AMY1 entry
Accession.status: Accession resolution status, including unchanged and demerged
Accession.candidates: List-column of candidate current UniProt accessions for historical entries; AMY1 has P0DUB6, P0DTE7 and P0DTE8

Details

The original Caprion annotations and accession identifiers are preserved. UniProt marks the historical AMY1 accession P04745 as demerged. The candidate current accessions P0DUB6, P0DTE7 and P0DTE8 are recorded for subsequent peptide-level evaluation. These candidates do not establish that all three sequences contributed to the original protein quantification. See the Caprion repository for details of its use.

Source

Caprion pilot-study annotations and UniProt accession information.

Olink/INF1 panel

Description

The panel is based on SCALLOP-INF as in Zhao et al. (2023).

Usage

data(inf1)

Format

A data frame with 92 rows and 9 variables:

uniprot: UniProt id
prot: Protein
target: Protein target name
target.short: Protein target short name
gene: HGNC symbol
chr: chromosome (1-13,16-17,19-22)
start: start
end: end
chromosome: updated chromosomes
start38: start position under build 38
end38: end position under build 38
ensGene: Ensembl gene name
ensembl_gene_id: ENSEMBL gene
alt_name: recent name from www.uniprot.org

Details

Assembled for SCALLOP-INF

References

Zhao JH, Stacey D, Eriksson N, Macdonald-Dunlop E, Hedman ÅK, Kalnapenkis A, Enroth S, Cozzetto D, Digby-Bell J, Marten J, Folkersen L, Herder C, Jonsson L, Bergen SE, Gieger C, Needham EJ, Surendran P, Team EBR, Paul DS, Polasek O, Thorand B, Grallert H, Roden M, Võsa U, Esko T, Hayward C, Johansson Å, Gyllensten U, Powell N, Hansson O, Mattsson-Carlgren N, Joshi PK, Danesh J, Padyukov L, Klareskog L, Landén M, Wilson JF, Siegbahn A, Wallentin L, Mälarstig A, Butterworth AS, Peters JE (2023). “Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets.” Nature Immunology, 24(9), 1540-1551. doi:10.1038/s41590-023-01588-w.

Supplementary table 3

Description

Supplementary information for Zhao et al. (2023).

Usage

data(scallop_inf1)

Format

A data frame with 180 rows and 19 variables:

UniProt: UnitProt ID
Protein: Protein name
Protein_gene_symbol: Gene symbol
Chromosome: Chromosome
Position: Position
cistrans: cis/trans
rsid: reference sequence ID
Effect_allele: Effect allele
Other_allele: Eeference allele
EAF: Effect allele frequency
b: b
SE: SE
log10P: log10(P)
Direction: Direction field in METAL output
HetISq: I^2
HetChiSq: Heterogeneity chi-square
HetDf: degrees of freedom
logHetP: Heterogeneity log10(P)
N: N

References

Seer 1980 panel

Description

ST1 from Suhre et al. (2024).

Usage

data(seer1980)

Format

A data frame with 1,980 rows:

PID.NP: PID.NP
protein_ids: protein_ids
protein_names: protein_names
mapped.UniProtID: mapped.UniProtID
mapped_gene_id: mapped_gene_id
gene_name: gene_name
description: description
chr: chr
start: start
end: end

Details

As above.

References

Suhre K, Chen Q, Halama A, Mendez K, Dahlin A, Stephan N, Thareja G, Sarwath H, Guturu H, Dwaraka VB, Batzoglou S, Schmidt F, Lasky-Su JA (2024). “A genome-wide association study of mass spectrometry proteomics using the Seer Proteograph platform.” BioRxiv. doi:10.1101/2024.05.27.596028.

SWATH-MS panel

Description

As indicated by Ludwig et al. (2018), Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra (SWATH-MS) represents a specific variant of Data-Independent Acquisition (DIA). The panel shown here is curated during INTERVAL pilot study.

Usage

data(swath_ms)

Format

A data frame with 684 rows and 5 variables:

Accession: UniProt id
accList: List of UniProt ids
uniprotName: Protein
ensGene: ENSEMBL gene
geneName: HGNC symbol

Details

As above.

Package {pQTLdata}

A summary of datasets

Description

Details

Usage

Author(s)

References

See Also

Examples

Olink/Explore 1536 panel

Description

Usage

Format

Details

Olink/Explore 3072 panels

Description

Usage

Format

Details

Olink/Explore HT panels

Description

Usage

Format

Details

Olink/Target 96 panels

Description

Usage

Format

Details

Olink/qPCR panels

Description

Usage

Format

Details

SomaScan 11k

Description

Usage

Format

Details

Source

Somascan panel

Description

Usage

Format

Details

References

SomaScan v4.1

Description

Usage

Format

Details

Caprion panel

Description

Usage

Format

Details

Source

Olink/INF1 panel

Description

Usage

Format

Details

References

Supplementary table 3

Description

Usage

Format

References

Seer 1980 panel

Description

Usage

Format

Details

References

SWATH-MS panel

Description

Usage

Format

Details

References