Identify trait genes using sentinel SNPs generated from xQTLanalyze_getSentinelSnp

Source: R/analyze.R

Identify trait genes using sentinel SNPs generated from xQTLanalyze_getSentinelSnp

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

# \donttest{
# 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)
# }