get.prop.below.LLOD: Limit of detection analysis
In jinghuazhao/pQTLtools: A Protein Quantitative Trait Locus Toolkit

get.prop.below.LLOD

R Documentation

Limit of detection analysis

Description

The function obtains lower limit of detection as in proteomic analysis.

Usage

get.prop.below.LLOD(eset, flagged = "OUT")

Arguments

`eset`	An ExpressionSet object.
`flagged`	A flag is an indicator for sample exclusion.

Value

An updated ExpressionSet object.

Author(s)

James Peters

Examples

suppressMessages(library(Biobase))
data(sample.ExpressionSet, package="Biobase")
exampleSet <- sample.ExpressionSet
Biobase::fData(exampleSet)
Biobase::fData(exampleSet)$lod.max <-
    apply(Biobase::exprs(exampleSet),1,quantile,runif(nrow(exampleSet)))
lod <- get.prop.below.LLOD(exampleSet)
x <- dplyr::arrange(fData(lod),desc(pc.belowLOD.new))
knitr::kable(head(lod))
plot(x[,2], main="Random quantile cut off", ylab="<lod%")

jinghuazhao/pQTLtools documentation built on Nov. 21, 2024, 3:32 a.m.