I am using the fourCseq package to analyse 4C data, and I have several
- in the vignette you do precise that if too many fragments have no reads, this can result in a shift of the zscore distribution in negative value, making the distribution no more centred around 0, and therefore to a errors in the calculation of z-scores. If this is the cse, then the data are just too sparse to allow a proper calculation of the zscore and cannot be used? or is there anyway to correct it?
- is it possible to identify interraction in trans, ie on another chromosome? I could run the analysis on all the genome by specifyign all the chromosomes on the "referenceGenomeFile" arguments, but isn't does it biais the zscores calculation? (because most of the trans fragments should have no reads). Or is the fit used for the zscore calculation done only on the automatically/manually defined region around the view point when calling the function getZscores() ?
Many thanks in advance,
Computationnal systems biology Lab (Pr. Thieffry)
Institut of Biology at the Ecole Normale Superieure