pQTLdata: A summary of datasets
In pQTLdata: A Collection of Proteome Panels and Meta-Data

pQTLdata

R Documentation

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/) and 'Seer' (https://seer.bio/). 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) bioRxiv
`swath_ms`	SWATH-MS panel
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.

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

pQTLdata documentation built on April 12, 2025, 1:34 a.m.