Description Usage Arguments Value Author(s)
View source: R/HiCglmiProcData.R
This function is used to annotate Hi-C interaction bin pairs with genomic feature information such as ChIP-seq peak intervals.
1 2 | HiCglmiProcData(genomicFeatureList.GR, annotNames, HTCList, distInter,
filters.GR = NULL, filterMode = NULL, verbose = F)
|
genomicFeatureList.GR |
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). |
annotNames |
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. |
HTCList |
A HTClist object (HiTC R package). This object contains Hi-C intrachromosomal matrices. |
distInter |
Optional. A vector of two numerical values to set a distance range for Hi-C analysis. |
filters.GR |
Optional. A GRanges object. This is a set of genomic intervals to filter Hi-C data. |
filterMode |
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. |
verbose |
If verbose is True, then the different processing steps will be displayed. |
An object further used for HiCglmiModel function.
Raphael
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