In ComunidadBioInfo/HiConvert: What the Package Does (One Line, Title Case)

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Typically, data resulting from HiC experiments is analyzed either at the fragment level or summarized into genomic bins. Several analysis pipelines exist that enable users to characterize different aspects of their data, such as TADs, loops and compartments. However, each software uses their own formats and standarization of formats is currently lacking. This package provides a functions to convert between different software formats.

Converting between formats

Currently,

library(HiConvert)

Converting between fragment-level formats bams and bedpe files

The code below imports a bam file into R and stores it in a GenomicInteractions file.

in_file <- system.file( "extdata", "bam", "SRR400264_subset.bam",
                        package="HiConvert", mustWork=TRUE )
imported <- hic_import(in_file)
imported

The following code export a GI file into a bedpe.

hic_export( imported, file="prueba.bedpe" )
head( readLines( "prueba.bedpe" ) )

Converting between fragment-level formats bams and bedpe files

ComunidadBioInfo/HiConvert documentation built on Oct. 30, 2019, 5:44 a.m.