findCutoffs: Finding cutoffs

In mknoll/cnAnalysis450k: Copy Number Analysis for 450k Illumina Methylation Arrays

Description

Analyzes row-wise histograms by selecting the global maximum (0), as well as one further local maximum right (+) and left (-). Can make use of previous/following rows.

Usage

findCutoffs(data, zeichne = FALSE, ignoreNAs = FALSE, eps = 0.01,
  proximity = c(0, 0))

Arguments

data	Inputdata
zeichne	Debugging
ignoreNAs	F / T: if NAs occur, proceed, otherwise fail
eps	difference between x points (internal calculation)
proximity	how many previous / following rows should be considered for cutoff determination? c(prev, folw)

Value

identified cutoffs

Examples

candMatrix <- data.frame(
smp1=c(-0.097, -1.208,-0.134, 1.732),
smp2=c(-0.006, 0.004, 0.004, -0.001),
smp3=c(0.050, 0.008, 0.008,0.046 ))
rownames(candMatrix) <- c(
"chr1:15865", "chr1:110230252",
"chr1:110254692", "chr3:45838226"
)
findCutoffs(candMatrix, proximity=c(1,0))

mknoll/cnAnalysis450k documentation built on May 23, 2019, 2:01 a.m.