xQTLanalyze_getTraits | R Documentation |
xQTLanalyze_getSentinelSnp
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
)
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 |
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 |
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 |
A data.table object of one column of gencode ID. requiring overlapWithEGene is TRUE. |
A data.table object
# 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)
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