compareREDseq: Compare two RED Sequencing Dataset

Description Usage Arguments Value Author(s) See Also Examples

View source: R/compareREDseq.R

Description

For early stage experiment without replicates, compareREDseq outputs differentially cut RE sites between two experimental conditions using Fisher's Exact Test.

Usage

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compareREDseq(REsummary, col.count1 = 2, col.count2 = 3, multiAdj = TRUE,
 multiAdjMethod = "BH", maxP = 1, minCount = 1)

Arguments

REsummary

A matrix with a RE id column, 2 count/weight column, see examples

col.count1

The column where the total count/weight for the 1st experimental condition is

col.count2

The column where the total count/weight for the 2nd experimental condition is

multiAdj

Whether apply multiple hypothesis testing adjustment, TURE or FALSE

multiAdjMethod

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

maxP

The maximum p-value to be considered to be significant

minCount

For a RE site to be included, the tag count from at least one of the experimental condictions >= minimumCount

Value

p.value

the p-value of the test

*.count

weight/count from the input column col.count1 and col.count2

*.total

total weight/count from input column col.count1 and col.count2

REid

the id of the restriction enzyme from the input

odds.ratio

an estimate of the odds ratio for 2nd experimental condition vs. 1st experimental condition

*.adjusted.p.value

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

Author(s)

Lihua Julie Zhu

See Also

binom.test.REDseq

Examples

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library(REDseq)
x= cbind(c("RE1", "RE2", "RE3", "RE4"), c(10,1,100, 0),c(5,5,50, 40))
colnames(x) = c("REid", "control", "treated")
compareREDseq(x)

Bioconductor-mirror/REDseq documentation built on May 31, 2017, 10:43 p.m.