segmentDataAbs: Define gain / loss with given cutoffs

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

Description

Use absolute cutoffs to create CNV gain / loss matrix.

Usage

segmentDataAbs(data, upper, lower, ylim = NULL, plot = TRUE)

Arguments

data	segmentMatrix, e.g. acquired with createSegmentMatrix
upper	Upper cutoff (+1)
lower	Lower cutoff (-1)
ylim	y-axis limits of cutoff plot
plot	Should the data be plotted? Might take a long time.

Value

matrix, containing -1,0,+1 for losses / gains

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"
)
segmentDataAbs(candMatrix, upper=0.1, lower=-0.15)

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