This function is used to annotate Hi-C interaction bin pairs with genomic feature information such as ChIP-seq peak intervals.
HiCglmiProcData(genomicFeatureList.GR, annotNames, HTCList, distInter,
filters.GR = NULL, filterMode = NULL, verbose = F)A list of GRanges objects. Each GRanges object has been built from either coordinate data using readGFBed function (for instance ChIP-seq peak coordinates or functional element coordinates).
A character vector defining the name of each genomic feature. Names should not comprise any special character such as ":/+-*^,;!?" because an internal R formula object is created inside the function borderAnalysisFun.
A HTClist object (HiTC R package). This object contains Hi-C intrachromosomal matrices.
Optional. A vector of two numerical values to set a distance range for Hi-C analysis.
Optional. A GRanges object. This is a set of genomic intervals to filter Hi-C data.
Optional. If filterMode=="in", only Hi-C pairs that are within intervals from filters.GR are kept. If filterMode=="out", only Hi-C pairs that are outside intervals from filters.GR are kept.
If verbose is True, then the different processing steps will be displayed.
An object further used for HiCglmiModel function.