exportC: Export 'HTCexp' object

In bioinfo-pf-curie/HiTC: High Throughput Chromosome Conformation Capture analysis

Description

Export HTCexp object to tab format

Usage

exportC(x, file, per.chromosome=FALSE, use.names=FALSE, header=FALSE)

Arguments

x	object that inherits from class HTCexp
file	character; the basename of the output file
per.chromosome	logical; export each contact maps in a different files (i.e one per chromosome pair)
use.names	if TRUE, keep the original row/colnames of the contact matrix
header	if TRUE, add an header with the package version and the date

Value

Three output files will be created ; 2 BED files for each genomic intervals, and one tab file. The standard format for 5C/Hi-C data is the following :
** One list file (tab delimited) bin1 bin2 x12 bin1 bin3 x13 ... ** The BED file(s) describing the intervals ('xgi.bed' and 'ygi.bed' are usually the same for Hi-C but can be different for 5C data) chr1 1 1000000 bin1 chr1 1000001 2000000 bin2 ... Note that this format is particularly interesting for sparse data as only non null values are stored. If per.chromosome=FALSE, the data will be exported in one genome scaled file.

Author(s)

N. Servant

See Also

export.my5C, importC

Examples

## Not run: 
data(Nora_5C)

## Data binning
E14.bin<-binningC(E14$chrXchrX)

## Export the new intervals definition
exportC(E14.bin, file="E14")

## End(Not run)

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