compareREDseq: Compare two RED Sequencing Dataset

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

Description

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

Usage

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

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)

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