binningC: Windowing of high-throughput 'C' contact matrix

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

View source: R/binningC.R

Description

Binning of 'C' contact map

Usage

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binningC(x, binsize=100000, bin.adjust=TRUE, upa=TRUE,
method=c("sum", "median","mean"), use.zero=TRUE, step=1, optimize.by = c("speed", "memory"))

Arguments

x

object that inherits from class HTCexp

binsize

size of the bin to consider for windowing

bin.adjust

logical; adjust the size of the bin to the size of the genomic region

upa

logical; unique primer assignment. Allow one primer to belong to one or several bins

method

the method used to combine the counts. Must be ‘mean’, ‘median’ or ‘sum’

use.zero

logical; use the zero values in the method calculation

step

numeric; binning step size in n coverage i.e. window step

optimize.by

"speed" will use faster methods but more RAM, and "memory" will be slower, but require less RAM

Details

bin.adjust allows to work with bins of exactly the same size. Otherwise, the last bin is usually smaller than the others.
This function aims at changing the resolution of both 5C or Hi-C data. In case of 5C data (i.e. raw, not binned data), the contacts between all pairs of primers will be summarized per genomic bins (the median of all pairwise primers is usually used). In case of binned data (as Hi-C maps), the function can generate smaller resolution maps by aggregating bins. For instance, going from a 40kb resolution to a 1Mb resolution.
The method is used to combine the counts in a bin, must be ‘mean’, ‘median’ or ‘sum’. The step parameter allows to choose the overlap between the bins. A step of 2 means a 50% overlap between two bins, a step of 3 means a 60% overlap between two bins, etc.

Value

An HTCexp-class object with binned intraction data. In this case, the genomic intervals are converted into bins of fixed size. The contact matrix is symetric.

Author(s)

N. Servant, B. Lajoie

See Also

HTCexp-class

Examples

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data(Nora_5C)

## Data binning 100kb, with a 1/3 overlap
E14.bin <- binningC(E14$chrXchrX, binsize=100000, step=3)
show(E14.bin)
## Move to a lower resolution map
E14.bin2 <- binningC(E14.bin, binsize=500000, step=1)
show(E14.bin2)

bioinfo-pf-curie/HiTC documentation built on May 17, 2019, 6:39 p.m.