createSegmentMatrix: Create Segment-Matrix

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

Description

Create Segment Matrix from Segment-list (created with findSegments())

Usage

createSegmentMatrix(data, p.select = 0.05, arrayType = "auto")

Arguments

data	input data
p.select	0.05 selection of candidates which have a p.value < p.select for at least 1 sample
arrayType	"auto","450k", "EPIC"; auto -> tries to automatically determine the array type (450k, EPIC)

Value

all aligned segments

Examples

data <- data.frame(
chr=rep("chr1", 4),
startCG=c("cg13869341","cg08651003", "cg26542962", "cg11680055"),
endCG=c("cg01729401", "cg00373247", "cg20944548", "cg25520068"),
median=c(-0.09, -0.11, -0.16, -1.21),
mean=c(-0.09, -0.12, -0.17, -1.75),
sd=c(0.13, 0.17, 0.2, 2.1),
smp=rep("5723646053_R04C02", 4),
p.val=rep(0.00006, 4)
)
createSegmentMatrix(data)

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