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ObjectsDescription
Datasets
biomaRtCurated data from biomaRt
caprionCaprion panel
hg19Curated data from Bioconductor
hg19TablesCurated data from UCSC genome browser
inf1Olink/INF panel
Olink_NGSOlink/NGS panels
Olink_qPCROlink/qPCR panels
SomaLogic160410SomaLogic panel
SomaScanV4.1SomaScan v4.1 panel
st4ST4 of the INTERVAL SomaLogic paper
st6ST6 of the INTERVAL SomaLogic paper
st18ST18 of the INTERVAL SomaLogic paper
swath_msSWATH-MS panel
eQTL/GWAS
get.prop.below.LLODLimit of detection analysis
import_eQTLCatalogueImport eQTL Catalogue
import_OpenGWASImport OpenGWAS
make_ExpressionSetA call to ExpressionSet class
novelty_checkLocus novelty check
run_colocColocalisation analysis
MR analysis
pqtlMRBidirectional pQTL-MR analysis
qtl_lookupQTL lookup
run_TwoSampleMRA generic wrapper for TwoSampleMR analysis
PhenoScanner Utilities
genequeriesphenoscanner genequeries in batches
regionqueriesphenoscanner regionqueries in batches
snpqueriesphenoscanner snpqueries in batches
UniProt API
uniprot2idsUniProt ID to others
Functions in R/gap
METAL_forestplotForest plots from metal analysis
cis.vs.trans.classificationa cis/trans classifier
circos.cis.vs.trans.plotcircos plot of cis/trans classification
circos.mhtplotcircos Manhattan plot with gene annotation
circos.mhtplot2Another circos Manhattan plot
csCredible set
get_b_seGet b and se from AF, n, and z
get_pve_seGet pve and its standard error from n, z
get_sdyGet sd(y) from AF, n, b, se
gsmrMendelian randomization analysis
invnormalInverse normal transformation
log10plog10(p) for a standard normal deviate
log10pvaluelog10(p) for a P value including its scientific format
logplog(p) for a normal deviate
mhtplot.truncTruncated Manhattan plot
miamiplot2Miami plot
mr_forestplotMendelian Randomization forest plot
qtlClassifierA QTL cis/trans classifier
qtl2dplot2D QTL plot
qtl2dplotly2D QTL plotly
qtl3dplotly3D QTL plotly

Details

Some generic description for the datasets are as follows.

chr

chromosome

start

Start position

end

End position

gene

Gene name

UniProt

UniProt ID

Author

Jing Hua Zhao in collaboration with other colleagues

Examples

if (FALSE) {
# datasets
head(biomaRt)

# Olink-SomaLogic panel overlap
p <- list(setdiff(inf1$uniprot,"P23560"),
          setdiff(SomaLogic160410$UniProt[!is.na(SomaLogic160410$UniProt)],"P23560"))
cnames <- c("INF1","SomaLogic")
VennDiagram::venn.diagram(x = p, category.names=cnames,
                          filename='os.png', imagetype="png", output=TRUE)
m <- merge(inf1,SomaLogic160410,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(SomaLogic160410[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 SomaLogic 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)
}