calculate genomic control inflation factor — xQTLanalyze_calLambda • xQTLbiolinks

calculate genomic control inflation factor

xQTLanalyze_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 <- "https://raw.githubusercontent.com/dingruofan/exampleData/master/eqtl/MMP7_qtlDF.txt"
qtl <- data.table::fread(url1, sep="\t")

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

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