CQC {HiTC} | R Documentation |
Quality Control for high-throughput 'C' experiment
CQC(x, cis.trans.ratio = TRUE, hist.interac=TRUE, scat.interac.dist=TRUE, hist.dist=TRUE, trim.range=0.98, winsize=NA, dev.new=TRUE)
x |
object that inherits from class
|
cis.trans.ratio |
logical; barplot of percentage of inter-intrachromsomal interactions |
hist.interac |
logical; histogram of the interaction frequency |
scat.interac.dist |
logical; scatter plot of interaction count versus the genomic distance between two elements |
hist.dist |
logical; histogram of the distance between the 'x' and 'y' intervals |
trim.range |
remove the extreme values by trimming the counts. Only use for plotting functions. [0,1] |
winsize |
used for the scat.interac.dist. If specify, the data are windowed before plotting |
dev.new |
if true, each graphs is plotted in a new device |
If x
is a HTClist
object, all HTCexp
objects are merged.
The zero values are not used to compute the descriptive statistics and to display the data.
If trim.range
are lower than 1. The highest values (quantile probability is equal to trim.range
) are discarded.
Create quality plots and return a matrix
with some simple statistics on all, cis and trans data.
N. Servant, B. Lajoie
data(Nora_5C) ## Quality Control CQC(E14)