parseRaoHiCtoGI: Parse Hi-C interactions from Rao et. al 2014 as...
In ibn-salem/chromint: Analysis of Chromatin Interactions

This function parses interactions from a single experiment by a given resolution. It takes a path to a directory with uncompressed raw data and subdirectories for each cell-type. The data can be manually downloaded and from this url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63525.

1 2	parseRaoHiCtoGI(cell, resolution, baseDir, seqInfo, interChromosomal = TRUE, normalizeByExpected = FALSE, mapQual = "MAPQGE30", norm = NULL)

`cell`	The cell type of the input experiment
`resolution`	The matrix resolution of the Hi-C map in bp
`baseDir`	The path to the directory with the Hi-C data.
`seqInfo`	A seqinfo object of the genome.
`interChromosomal`	logical idicating whether inter-chromosomal contacts should be parsed.
`normalizeByExpected`	Should contact frequencies be normalized by distance. Default is FALSE.
`mapQual`	character representing the mapping quality threshold. Defualt is "MAPQGE30".
`norm`	character representation of the normalization method to use. Default is NULL meaning that no normalization is applied. Possible values are "KR" or "VC". This is not impplemented yet.