Exploring the genetic correlation between inflammatory bowel disease and psychiatric disorders: insights from genome-wide association studies.
Paper
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The authors' code
R · 52 lines · 2.5 KB · no license
- #设置当前工作路径
- setwd("D:/5.TWAS_UTMOST/07.UTMOST")
- #清除一切变量
- rm(list=ls())
- #释放不再使用的内存
- gc()
- #显式路径
- getwd()
- #显示R包安装位置
- .libPaths()
- #加载包
- library(Fast2TWAS)
- #输入参数
- trait="Prostate cancer"
- #UTMOST软件执行TWAS分析，获取GTExV8中单个组织中基因与疾病之间的TWAS分析结果-----
- ################################################################################
- ###########################该步骤很耗时间请耐心等待#############################
- ################################################################################
- UTMOST_single=TWAS_UTMOST_single_tissue(gwasfile='../06.pre_data/Prostate cancer.txt',
- db_path_dir= "../03.reference/UTMOST/database_normalized_pruned/",
- covariance_path_dir = "../03.reference/UTMOST/covariance_GTEx8_normalized_pruned/",
- outname = paste0(trait,"_GTExv8"),
- tissue="GTExv8",
- SNP = "SNP",
- effect_allele = "effect_allele",
- other_allele = "other_allele",
- BETA = "beta",
- pval = "pval",
- flag_options=NULL,
- force = F,
- nthread = 8)
- #UTMOST软件执行TWAS分析,计算GTExV8中跨组织联合测试关联结果----------------------
- ################################################################################
- ###########windows系统中该程序可能多次运行都不成功，请耐心多试几次##############
- ################################################################################
- UTMOST_cross=TWAS_UTMOST_cross_tissue(db_path_dir =paste0(dirname(getwd()),"/03.reference/UTMOST/database_normalized_pruned/"),
- covariance_joint_path_dir = paste0(dirname(getwd()),"/03.reference/UTMOST/covariance_joint_GTEx8_normalized_pruned"),
- gene_info_file = "./result/gene_info_GTExv8.txt",
- flag_options=NULL,
- outname = paste0(trait,"_GTEXv8_49_cross"),
- force = F)
07.UTMOST.R at commit bf0dd5a, no license · at the source
Overview
Abstract
The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.
Repository
Its files are read in the Code ↔ Paper reader above.
duanxian0301/TWAS
bf0dd5ad47dd0c1772856067207fd1d8962f17bf, 15 January 2025Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
18 files
- 07.UTMOST.R, R, 52 lines
- 08.UTMOST_ensTOsymble.R, R, 79 lines
- 09.sig_cross_UTMOST.R, R, 46 lines
- 10.FUSION.R, R, 37 lines
- 11.FUSION_ensTOsymble.R, R, 39 lines
- 12.sig_FUSION.R, R, 48 lines
- 13.FUSION_manhattan.R, R, 55 lines
- 14.MAGMA.R, R, 44 lines
- 15.plot_MAGMA.R, R, 195 lines
- 16.intersect_UTMOST_FUSI
ON.R , R, 51 lines - 17.Joint_conditional.R, R, 58 lines
- 18.FOCUS.R, R, 60 lines
- 19.Venn_UTMOST_FUSION_MA
GMA_FOCUS.R , R, 83 lines - 20.pre_eqtlsum_from_GTEx
.R , R, 79 lines - 21.pre_eqtlsum_hg38Tohg1
9.R , R, 50 lines - 22.Colocalization.R, R, 99 lines
- 23.mendelian_randomizati
on.R , R, 58 lines - 24.plotMR.R, R, 180 lines
The paper's code and data availability statement is in the Data section.
Tracing map
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- 18 scripts, each with its path and the digest of its content;
- no match between paragraphs and code yet;
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
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Code and data availability statement
The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:
- it points to the authors' code: duanxian0301/
TWAS
Read it in the paper: doi.org/10.1007/s00406-026-02302-1.
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Version 2, 28 September 2026
- Publisher: n/a → Springer Science+Business Media
Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 3 authors, 6 keywords, 8 MeSH terms, 1 funder, 61 references.
Cite
This paper
Zhang, J., Shen, J., & Liu, L. (2026). Exploring the genetic correlation between inflammatory bowel disease and psychiatric disorders: insights from genome-wide association studies. European archives of psychiatry and clinical neuroscience, 276(7), 3417-3431. https://
BibTeX
@article{zhang2026explor
author = {Zhang, Jie and Shen, Jing and Liu, Lifeng},
title = {{Exploring the genetic correlation between inflammatory bowel disease and psychiatric disorders: insights from genome-wide association studies}},
journal = {European archives of psychiatry and clinical neuroscience},
year = {2026},
month = jun,
volume = {276},
number = {7},
pages = {3417--3431},
publisher = {Springer Science+Business Media},
issn = {0940-1334},
doi = {10.1007/
url = {https://
pmid = {42362821},
pmcid = {PMC13562344}
}
RIS
TY - JOUR
AU - Zhang, Jie
AU - Shen, Jing
AU - Liu, Lifeng
TI - Exploring the genetic correlation between inflammatory bowel disease and psychiatric disorders: insights from genome-wide association studies
T2 - European archives of psychiatry and clinical neuroscience
J2 - Eur Arch Psychiatry Clin Neurosci
PY - 2026
DA - 2026/
VL - 276
IS - 7
SP - 3417
EP - 3431
SN - 0940-1334
PB - Springer Science+Business Media
DO - 10.1007/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1007/
"type": "article-journal",
"title": "Exploring the genetic correlation between inflammatory bowel disease and psychiatric disorders: insights from genome-wide association studies",
"container-title": "European archives of psychiatry and clinical neuroscience",
"author": [
{
"family": "Zhang",
"given": "Jie"
},
{
"family": "Shen",
"given": "Jing"
},
{
"family": "Liu",
"given": "Lifeng"
}
],
"container-title-short":
"volume": "276",
"issue": "7",
"page": "3417-3431",
"DOI": "10.1007/
"PMID": "42362821",
"PMCID": "PMC13562344",
"ISSN": "0940-1334",
"publisher": "Springer Science+Business Media",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
6,
26
]
]
}
}
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