Package: loopQTL 0.99.0

Rhie Lab at the University of Southern California

loopQTL: Anchor-Restricted Loop QTL Mapping from Hi-C

Maps chromatin loop QTLs by testing whether genotype at a loop's anchors associates with the loop's contact strength across samples. Reads .hic files via strawr, builds an exact-coordinate consensus loop set, normalizes contact strength across samples via band-wise quantile normalization in the style of BNBC (implemented on top of preprocessCore), and runs anchor-restricted SNP-by-loop regressions with MatrixEQTL. Intra-chromosomal loops only; no FDR or lead-SNP selection (left to the user).

Authors:Rhie Lab at the University of Southern California [cre], Zexun Wu [aut]

loopQTL_0.99.0.tar.gz
loopQTL_0.99.0.zip(r-4.7-any)loopQTL_0.99.0.zip(r-4.6-any)loopQTL_0.99.0.zip(r-4.5-any)
loopQTL_0.99.0.tgz(r-4.6-any)loopQTL_0.99.0.tgz(r-4.5-any)
loopQTL_0.99.0.tar.gz(r-4.7-any)loopQTL_0.99.0.tar.gz(r-4.6-any)
loopQTL_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
loopQTL/json (API)

# Install 'loopQTL' in R:

install.packages('loopQTL', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rhielab/loopqtl/issues

On CRAN:

software dna3dstructure epigenetics hic quantitativetraillocus snp

3.78 score 19 exports 86 dependencies

Last updated from:cc881e77e9. Checks:8 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	197
linux-devel	WARNING	330
source / vignettes	OK	295
linux-release	WARNING	279
macos-release	WARNING	211
macos-oldrel	WARNING	179
windows-devel	WARNING	219
windows-release	WARNING	229
windows-oldrel	WARNING	277
wasm-release	OK	151

Exports:cis loopQTLannotate loopQTLchooseK loopQTLExampleData loopQTLnormalize loopQTLpairData loopQTLplotLocus loopQTLplotPair loopQTLplotSnpWindow loopQTLsetup loops metadata phenotype resolution results runQTL samples show vcfPath

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli codetools cpp11 crayon curl data.table DBI DelayedArray farver fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable httr InteractionSet IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle Matrix MatrixEQTL MatrixGenerics matrixStats memoise mime openssl patchwork pkgconfig png preprocessCore R6 RColorBrewer Rcpp RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray strawr SummarizedExperiment sys VariantAnnotation vctrs viridisLite withr XML XVector yaml

Using loopQTL

Introduction | Acquiring and installing loopQTL and associated packages | System requirements | FIXME: update for 26/04 - recheck | Installation | Overview | loopQTLsetup: Validate inputs and build loopQTL object | loopQTLnormalize: Cross-normalization on Hi-C signal | loopQTLchooseK: Auto-select the number of PCs for covariates | runQTL: Anchor-restricted association testing | loopQTLpairData: Sample-level view of one loop × SNP pair | loopQTLannotate: Annotate results with target genes and regulatory peaks | loopQTLplotPair: Boxplot of loop strength by SNP dosage | loopQTLplotLocus: Locus-level track view of loops, SNPs, and genes | loopQTLplotSnpWindow: Hi-C-style beta heatmap around a SNP | Session info

Rendered fromloopQTL.Rmdusingknitr::rmarkdown

Last update: 2026-09-19
Started: 2026-09-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Class to store loopQTL input data and analysis results	cis cis,loopQTL-method loopQTL-class loops loops,loopQTL-method metadata metadata,loopQTL-method phenotype phenotype,loopQTL-method resolution resolution,loopQTL-method results results,loopQTL-method samples samples,loopQTL-method show,loopQTL-method vcfPath vcfPath,loopQTL-method
Annotate loopQTL results with target genes and regulatory peaks	loopQTLannotate
Auto-select the number of PCs for covariates	loopQTLchooseK
Load the bundled example loopQTL object	loopQTLExampleData
Cross-normalization on Hi-C signal	loopQTLnormalize
Sample-level view of one loop × SNP pair	loopQTLpairData
Locus-level track view of loops, SNPs, and genes	loopQTLplotLocus
Per-sample boxplot for a single SNP-loop pair	loopQTLplotPair
Hi-C-style beta heatmap around a SNP	loopQTLplotSnpWindow
Validate inputs and build loopQTL object	loopQTLsetup
Anchor-restricted association testing	runQTL