exportC {HiTC} | R Documentation |
HTCexp
objectExport HTCexp
object to tab format
exportC(x, file, per.chromosome=FALSE, use.names=FALSE, header=FALSE)
x |
object that inherits from class |
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 |
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.
N. Servant
## 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)