xQTLanno_calLambda: calculate genomic control inflation factor for a QTL/GWAS...
In xQTLbiolinks: An R Package for Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'
xQTLanno_calLambda R Documentation
calculate genomic control inflation factor for a QTL/GWAS summary statistics dataset.
Description
calculate genomic control inflation factor for a QTL/GWAS summary statistics dataset.
Usage
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
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$groups <- sample(c(0,1),size = nrow(qtl), replace = TRUE)
xQTLanno_calLambda(qtl[,.(pValue, groups)])
xQTLbiolinks documentation built on Sept. 15, 2023, 1:06 a.m.
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| xQTLanno_calLambda | R Documentation |
calculate genomic control inflation factor for a QTL/GWAS summary statistics dataset.
Description
calculate genomic control inflation factor for a QTL/GWAS summary statistics dataset.
Usage
xQTLanno_calLambda(summaryDT)
Arguments
summaryDT |
A data.frame containing one or two columns: p-value (required) and group (optional) |
Value
A data.table object
Examples
url1 <- "http://bioinfo.szbl.ac.cn/xQTL_biolinks/xqtl_data/eqtl/MMP7_qtlDF.txt"
qtl <- data.table::fread(url1, sep="\t")
# calculate lambda value with all variants
xQTLanno_calLambda(qtl[,.(pValue)])
# calculate lambda value for each group:
qtl$groups <- sample(c(0,1),size = nrow(qtl), replace = TRUE)
xQTLanno_calLambda(qtl[,.(pValue, groups)])
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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