binom.test.REDseq: Binomial test for REDseq dataset

In REDseq: Analysis of high-throughput sequencing data processed by restriction enzyme digestion

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

Author(s)

Lihua Julie Zhu

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)

REDseq documentation built on Nov. 8, 2020, 8:19 p.m.