compareREDseq {REDseq} | R Documentation |
For early stage experiment without replicates, compareREDseq outputs differentially cut RE sites between two experimental conditions using Fisher's Exact Test.
compareREDseq(REsummary, col.count1 = 2, col.count2 = 3, multiAdj = TRUE, multiAdjMethod = "BH", maxP = 1, minCount = 1)
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 |
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 |
Lihua Julie Zhu
binom.test.REDseq
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)