xQTLanalyze_getTraits: Identify trait genes using sentinel SNPs generated from...

In xQTLbiolinks: An R Package for Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'

Identify trait genes using sentinel SNPs generated from xQTLanalyze_getSentinelSnp

Description

Identify trait genes using sentinel SNPs generated from xQTLanalyze_getSentinelSnp

Usage

xQTLanalyze_getTraits(
  sentinelSnpDF,
  detectRange = 1e+06,
  tissueSiteDetail = "",
  genomeVersion = "grch38",
  grch37To38 = FALSE,
  overlapWithEGene = TRUE,
  egeneDF = NULL
)

Arguments

sentinelSnpDF	A data.table. Better be the results from the function "xQTLanalyze_getSentinelSnp", seven columns are required, including "rsid", "chr", "position", "pValue", "maf", "beta" and "se".
detectRange	A integer value. Trait genes that harbor sentinel SNPs located in the 1kb range upstream and downstream of gene. Default: 1e6 bp
tissueSiteDetail	(character) details of tissues in GTEx can be listed using tissueSiteDetailGTExv8 or tissueSiteDetailGTExv7
genomeVersion	"grch38" or "grch37". Default: "grch38"
grch37To38	TRUE or FALSE, we recommend converting grch37 to grch38, or using a input file of grch38 directly. Package rtracklayer is required.
overlapWithEGene	TRUE(default) of FALSE. take the intersection with eGenes, egene data.frame will be automatically download from GTEx, or can be provided by the parameter egeneDF specified the data.frame of one column of genecode ID. Default:TRUE
egeneDF	A data.table object of one column of gencode ID. requiring overlapWithEGene is TRUE.

Value

A data.table object

Examples

# without a customized egene file,
URL1<-"https://gitee.com/stronghoney/exampleData/raw/master/gwas/GLGC_CG0052/sentinelSnpDF.txt"
sentinelSnpDF <- data.table::fread(URL1)
traitsAll <- xQTLanalyze_getTraits(sentinelSnpDF, detectRange=1e4,"Brain - Cerebellum",
                                   genomeVersion="grch37", grch37To38=TRUE)
# with a egene file:
egeneFile <- "http://bioinfo.szbl.ac.cn/xQTL_biolinks/xqtl_data/egeneDF.txt"
egeneDF <- data.table::fread(egeneFile)
traitsAll <- xQTLanalyze_getTraits(sentinelSnpDF, detectRange=1e4,"Brain - Cerebellum",
                                   genomeVersion="grch37", grch37To38=TRUE, egeneDF=egeneDF)

xQTLbiolinks documentation built on Sept. 15, 2023, 1:06 a.m.