import.my5C {HiTC} | R Documentation

## Import data from my5C webtool

### Description

Import data from my5C webtool

### Usage

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

### Arguments

`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

### Details

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.

### Value

A `HTClist` object

### Author(s)

N. Servant

### See Also

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

### Examples

    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)

[Package HiTC version 1.38.0 Index]