Calculate genomic control inflation factor for a QTL/GWAS summary statistics dataset — xQTLanno_calLambda • xQTLbiolinks

Calculate genomic control inflation factor for a QTL/GWAS summary statistics dataset

xQTLanno_calLambda(summaryDT)

Arguments

summaryDT: A data.frame containing one or two columns: p-value (required) and group (optional)

Value

A data.table object

Examples

# \donttest{
url1 <- "http://bioinfo.szbl.ac.cn/xQTL_biolinks/xqtl_data/eqtl/MMP7_qtlDF.txt"
qtl <- data.table::fread(url1, sep="\t")

# calculate lambda value with all variants
xQTLanno_calLambda(qtl[,.(pValue)])

# calculate lambda value for each group:
qtl$groups <- sample(c(0,1),size = nrow(qtl), replace = TRUE)
xQTLanno_calLambda(qtl[,.(pValue, groups)])
# }