REDseq (version 1.18.0)

binom.test.REDseq: Binomial test for REDseq dataset

Description

For any early stage experiment with one experimental condition and one biological replicate, binom.test.REDseq computes p-value for each RE site in the genome.

Usage

binom.test.REDseq(REsummary, col.count = 2, multiAdj = TRUE, 
multiAdjMethod = "BH", prior.p = 0.000001)

Arguments

REsummary

A matrix returned from summarizeByRE with a RE id column, a count/weight column. See examples

col.count

The column where the total count/weight is

multiAdj

Whether apply multiple hypothesis testing adjustment, TURE or FALSE

multiAdjMethod

Multiple testing procedures, for details, see mt.rawp2adjp in multtest package

prior.p

It is the probability of assigning a mapped sequence tag to a given RE site. Assuming each RE site gets cut equally, then the prior.p = 1/number of total RE sites in the genome.

Value

p.value

p-value of the test

*.count

weight/count from the input REsummary

REid

the id of the restriction enzyme from the input REsummary

cut.frequency

cut frequency

*.adjusted.p.value

applicable if multiAdj=TRUE, adjusted p.value using * method specified in multiAdjMethod

See Also

compareREDseq

Examples

	library(REDseq)
	REsummary = cbind(c("RE1", "RE2", "RE3"), c(10,1,100))
	colnames(REsummary) = c("REid", "control")
	binom.test.REDseq(REsummary)