getTxValues: Get TX CNV values

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

Description

Calculates CN values for given list of transcripts.

Usage

getTxValues(data, ctrl, ctrlAll, tx, output = "diff",
  statistic = "wilcoxon", op = "median", arrayType = "auto")

Arguments

data	input data
ctrl	control data
ctrlAll	CN data of all control samples
tx	vector of list of transcripts#'
output	"ratio" (Sample/Ctrl) or "diff" (Sample-Ctrl)
statistic	statistics test to compare groups (controls vs smp); "t.test" or "wilcoxon" (Mann-Whitney-U Test)
op	median or mean
arrayType	"auto","450k", "EPIC"; auto -> tries to automatically determine the array type (450k, EPIC)

Value

list with tx-names, p-values and used statistical test

Examples

data <- data.frame(
smp1=c(-8.12, -5.225, -3.24, -3.62),
smp2=c(-5.0, -3.98, -4.06, -4.5),
smp3=c(NA, -2.48, -2.27, -2.1)
)
ctrlAll <- data.frame(
ctl1=c(1.0, -3.6, 0.7, -0.73),
ctl2=c(-0.4, -4.1, -4.2, -3.9),
ctl2=c(0.74, -1.12, -2.8, -1.67)
)
rownames(data) <- c(
"cg05132306", "cg15527168",
"cg17434257", "cg17592667"
)
rownames(ctrlAll) <- rownames(data)
ctrl <- c(0.74, -3.6, -2.8, -1.67)
#ctrl <- apply(ctrlAll, 1, "median")
names(ctrl) <- rownames(data)
getTxValues(data, ctrl, ctrlAll, "uc001aih.1", arrayType="450k")

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