about.Rmd

---
title: "About Data"
---

Output format from chicane run.

* target.id <- Target fragment involved in the interaction in the format of chromosome:start-end
* bait.id <- Bait fragment involved in the interaction, same format as target.id
* target.chr <- Chromosome of target fragment
* target.start <- Start position of target fragment
* target.end <- End position of target fragment
* bait.chr <- Chromosome of bait fragment
* bait.start <- Start position of bait fragment
* bait.end <- End position of bait fragment
* bait.to.bait <- Logical indicating if the interaction is between two bait fragments
* count.n <- Number of counts in replicate n (where n represents replicate number, this will appear for each replicate              included in a call that includes replicate merging)
* bait.trans.count<-Number of counts between bait fragment and fragments on another chromosome
* target.trans.count <- Number of counts between target fragment and fragments on another chromosome
* distance <- Distance in bp between center of bait fragment and center of target fragment on same chromosome (cis).                NA indicates fragments on different chromosomes (trans)
* count <- Sum of the counts from all replicates (observed)
* expected <- Counts expected by the model
* p.value <- P-value of observed vs. expected counts
* q.value <- Multiple testing corrected P-value