import.my5C: Import data from my5C webtool
In bioinfo-pf-curie/HiTC: High Throughput Chromosome Conformation Capture analysis

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

Import data from my5C webtool

1	import.my5C(file, allPairwise=FALSE, rm.trans=FALSE, lazyload=FALSE)

`file`	input file from the my5C webtool
`allPairwise`	logical; generate all pairwise chromosomal contact maps, i.e chr1-chr2, chr2-chr1
`rm.trans`	if true, only intra-chromosomal maps are loaded
`lazyload`	logical; force the intra-chromosomal contact maps to be stored as triangular matrix

This function allows data import from the the my5C webtool.
The matrix format is a tab-delimited format, corresponding to the contact map. The rownames and columnames are splitted to created the genome intervals (example : REV_2|mm9|chrX:98831149-98834145).

The allPairwise option is not necessary in case of symetric design. Otherwise, it will return all the pairwise contact maps.

The matrix will be stored as a matrix inheriting from Matrix class. If forcesymmetrical=TRUE, the intrachromosomal matrix as coerced to symmetricMatrix class allowing a much more efficient memory usage.

A HTClist object

N. Servant

HTClist-class,HTCexp-class,importC, Matrix-class, symmetricMatrix-class

exDir <- system.file("extdata", package="HiTC")
## Load my5C matrix format
hiC<-import.my5C(file.path(exDir,"HIC_gm06690_chr14_chr14_1000000_obs.txt"))
detail(hiC)