CQC: Quality Control for high-throughput 'C' experiment

In HiTC: High Throughput Chromosome Conformation Capture analysis

Description

Quality Control for high-throughput 'C' experiment

Usage

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)

Arguments

x	object that inherits from class HTCexp or HTClist
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

Details

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.

Value

Create quality plots and return a matrix with some simple statistics on all, cis and trans data.

Author(s)

N. Servant, B. Lajoie

See Also

HTCexp-class

Examples

data(Nora_5C)

## Quality Control
CQC(E14)

HiTC documentation built on Nov. 8, 2020, 8:27 p.m.