A summary of datasets

It gathers protein panel information and meta-data for pQTLtools, https://jinghuazhao.github.io/pQTLtools/.

Details

Available data are listed in the following table.

Objects	Description
Datasets
`biomaRt`	Curated data from biomaRt
`caprion`	Caprion panel
`hg19`	Curated data from Bioconductor
`hg19Tables`	Curated data from UCSC genome browser
`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_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
`st4`	ST4 of the INTERVAL SomaLogic paper
`st6`	ST6 of the INTERVAL SomaLogic paper
`st18`	ST18 of the INTERVAL SomaLogic paper
`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

Jing Hua Zhao in collaboration with other colleagues.

Examples

if (FALSE) { # \dontrun{
# See more on SCALLOP-INF at https://jinghuazhao.github.io/INF/
# datasets
head(biomaRt)

# Olink-SomaScan panel overlap
p <- list(setdiff(inf1$uniprot,"P23560"),
          setdiff(SomaScan160410$UniProt[!is.na(SomaScan160410$UniProt)],"P23560"))
cnames <- c("INF1","SomaScan")
VennDiagram::venn.diagram(x = p, category.names=cnames, filename=NULL,
                          disable.logging = TRUE, imagetype="png", output=TRUE)
m <- merge(inf1,SomaScan160410,by.x="uniprot",by.y="UniProt")
u <- setdiff(with(m,unique(uniprot)),"P23560")
options(width=220)
o <- subset(inf1,uniprot %in% u)
dim(o)
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

# SCALLOP/INF1
INF <- Sys.getenv("INF")
INF1_merge <- merge(inf1,
                    read.delim(file.path(INF,"work","INF1.merge-rsid"),as.is=TRUE),
                    by="prot")
INF1_uniprot <- unique(with(INF1_merge,uniprot))

# INTERVAL SomaScan data at box
HOME <- Sys.getenv("HOME")
box <- read.delim(file.path(HOME,"SomaLogic","doc","INTERVAL-box.tsv"),as.is=TRUE)
box_INF1 <- subset(box,UniProt %in% INF1_uniprot)
box_uniprot <- setdiff(unique(with(box_INF1,UniProt)),"P23560")
setdiff(INF1_uniprot,box_uniprot)

# Phenoscanner database
ps <- merge(subset(read.delim(file.path(INF,"work","pQTL_2018.txt.gz"),as.is=TRUE),
            pmid==29875488),
            box,by.x="trait",by.y="TargetFullName")
z <- subset(ps,UniProtgwas %in% INF1_uniprot & p<=1.5e-11)

# ST4 on Nature
st4regions <- subset(st4, UniProt %in% INF1_uniprot)
unique_uniprot_list <- setdiff(intersect(st4$UniProt,inf1$uniprot),"P23560")
subset(INF1_merge,uniprot %in% unique_uniprot_list)
} # }

Details

Usage

See also

Author

Examples