import.my5C: Import data from my5C webtool

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

View source: R/import.R

Description

Import data from my5C webtool

Usage

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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

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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)

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