HiCglmiProcData: Process data for further generalized linear regression with...

Description Usage Arguments Value Author(s)

View source: R/HiCglmiProcData.R

Description

This function is used to annotate Hi-C interaction bin pairs with genomic feature information such as ChIP-seq peak intervals.

Usage

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HiCglmiProcData(genomicFeatureList.GR, annotNames, HTCList, distInter, 
		filters.GR = NULL, filterMode = NULL, verbose = F)

Arguments

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.

Value

An object further used for HiCglmiModel function.

Author(s)

Raphael


HiCglmi documentation built on April 19, 2018, 1:04 a.m.