基因共定位 xQTLbiolinks 第4部分-CSDN博客

本文链接：https://blog.csdn.net/weixin_46587777/article/details/142535739

Developed by Ruofan Ding, Xudong Zou, Yangmei Qin, Gao Wang, Lei Li

xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs

xQTLbiolinks is a end-to-end bioinformatic tool for efficient mining and analyzing public and user-customized xQTLs data for the discovery of disease susceptibility genes. xQTLbiolinks consists of tailored functions that can be grouped into four modules: Data retrieval, Pre-processing, Analysis and Visualization.

Instructions, documentation, and tutorials can be found at here.

Quick Start

xQTLbiolinks can be installed and used on any operator systems supporting R. The latest version (v1.6.3) is also available at GitHub repository and it can be installed through devtools::install_github("dingruofan/xQTLbiolinks”). For more details, please refer to the instructions at Installation section below.
Find the Query and download for xQTLs, gene, variant, tissue, sample and expressions.
Find the Quick Start for a quick application of colocalization analysis with xQTLbiolinks. Go through a whole Case study of detection of casual vairants and genes in prostate cancer using xQTLbiolinks.
The details and instructions of all functions implemented in xQTLbiolinks can be found here. Find more instructions with examples for visualizations here.

Citation

If you find the xQTLbiolinks package or any of the source code in this repository useful for your work, please cite:

Ruofan Ding, Xudong Zou, Yangmei Qin, Lihai Gong, Hui Chen, Xuelian Ma, Shouhong Guang, Chen Yu, Gao Wang, Lei Li, xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs, Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad440,

Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China

Dependencies

The xQTLbiolinks package has the following dependencies:

R packages: BiocGenerics, cowplot (>= 1.1.1), curl (>= 4.3.2), data.table (>= 1.14.2), DBI, SummarizedExperiment, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2 (>= 3.3.6), ggrepel, IRanges, jsonlite (>= 1.7.2), viridis, RMySQL, stringr (>= 1.4.0), utils (>= 4.0.3),VariantAnnotation, TxDb.Hsapiens.UCSC.hg38.knownGene, PupillometryR, coloc, hyprcoloc, knitr, rtracklayer, usethis, ggridges, CMplot, R.utils, ggforestplot.

Installation

To install this R package, you will need to have required package SummarizedExperiment installed from Bioconductor with following command:

if (!require("BiocManager", quietly = TRUE)){install.packages("BiocManager")}
BiocManager::install("SummarizedExperiment") # For windows or linux
BiocManager::install("SummarizedExperiment",type="source") # For MAC

Once you have installed the required package, you can then install xQTLbiolinks from CRAN or github(recommended) using following command:

# Install from github to get the latest version.
if(!require("devtools")){install.packages("devtools")}
devtools::install_github("dingruofan/xQTLbiolinks")

4. Visualization using xQTLbiolinks

2023-05-01

Source: vignettes/visualization.Rmd

Some visual examples are provided in this vignette, including example data, code, and figures.

Visualilzation of eQTL, sQTL, gene expression across tissues.

xQTLvisual_eqtl("KIF15")

 genes <- c("FNDC8", "S100Z", "AQP6", "AMOT", "C3orf38", "FOXL1", "COX11", "FCN3", "DDX58", "CFI", "MS4A18", "NUDT13", "HOXA4", "VSX1")
 xQTLvisual_genesExp(genes, tissueSiteDetail="Lung")

geneExpTissues <- xQTLvisual_geneExpTissues("TP53", tissues=c("Lung", "Brain","Ovary"))

geneExpTissues <- xQTLvisual_geneExpTissues("TP53")

expEqtl <- xQTLvisual_eqtlExp(variantName="rs78378222", gene ="TP53",
                              tissueSiteDetail="Lung")
expEqtl

expSqtl <- xQTLvisual_sqtlExp(variantName="chr11_66561248_T_C_b38",variantType="variantId",
                              phenotypeId ="chr11:66348070:66353455:clu_8500:ENSG00000255468.6",
                              tissueSiteDetail="Skin - Sun Exposed (Lower leg)")
expSqtl

LocusZoom plot for GWAS dataset:

library(data.table)
gwasDF <- fread("https://gitee.com/stronghoney/exampleData/raw/master/gwasChr6Sub4.txt")
p_all <- xQTLvisual_locusZoom(gwasDF)
p_sub <- xQTLvisual_locusZoom(gwasDF, posRange="chr6:4.7e7-4.8e7", population ="EUR")
cowplot::plot_grid(p_all, p_sub, align = "h", ncol = 2)

LocusZoom plot for eQTL signals of a gene of interest:

eqtlAsso <- xQTLdownload_eqtlAllAsso("RP11-385F7.1",
                                     tissueLabel = "Brain - Cortex")
p_all <- xQTLvisual_locusZoom(eqtlAsso[,c("snpId", "chrom", "pos", "pValue")], highlightSnp="rs4711878" )
p_sub <- xQTLvisual_locusZoom(eqtlAsso[,c("snpId", "chrom", "pos", "pValue")], highlightSnp="rs4711878",
                              posRange="chr6:47.3e6-47.9e6")
cowplot::plot_grid(p_all, p_sub, align = "h", ncol = 2)

library(data.table)
eqtlDF <-fread("https://gitee.com/stronghoney/exampleData/raw/master/eqtl/eqtlAsso1.txt")
gwasDF <-fread("https://gitee.com/stronghoney/exampleData/raw/master/gwas/AD/gwasChr6Sub3.txt")
xQTLvisual_locusCompare( eqtlDF, gwasDF, legend_position="topleft")

gwasEqtldata <- data.table::fread("http://bioinfo.szbl.ac.cn/xQTL_biolinks/xqtl_data/gwas/AD/gwasEqtldata.txt")
xQTLvisual_locusCombine(gwasEqtldata, highlightSnp="rs13120565")

xQTLvisual_coloc( gene="MMP7", variantName="rs11568818", study="TwinsUK")

Developed by Ruofan Ding, Xudong Zou, Yangmei Qin, Gao Wang, Lei Li.