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

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/qualityControl.R

Description

Quality Control for high-throughput 'C' experiment

Usage

1
2
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

1
2
3
4
data(Nora_5C)

## Quality Control
CQC(E14)

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