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This function is for internal use only! The function computes the average value of a genomic feature for each bin of size binsize.
● Data Source:
CranContrib
● Keywords:
● Alias: averagePerBin
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This is the main function. This function estimates the influences of genomic features on chromatin domain borders by a multiple logistic regression model. Enrichment test by simple logistic regression is also included in this function for comparisons. Genomic features can be either coordinate data (e.g. ChIP-seq peak or functional element coordinates) or quantitative data (e.g. normalized ChIP-seq values: log2(ChIP/Input) values). The proposed method is flexible and can account for statistical interactions among multiple genomic features.
● Data Source:
CranContrib
● Keywords:
● Alias: borderAnalysisFun
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Function to import a genomic feature wig or bigWig file. The file can contain for instance normalized ChIP-seq values (log2(ChIP/Input) values).
● Data Source:
CranContrib
● Keywords:
● Alias: readGFWig
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Function to import a chromatin domain bed file. The bed file must contain coordinates of the chromatin domains. It can be for instance topologically associating domain (TAD) coordinates. In the bed file, the first column is the chromosome, the second column is the starting position of the domain, the third column is the ending position of the domain. The fourth column (optional) is the annotation of the domain (for instance: active, PcG, ...).
● Data Source:
CranContrib
● Keywords:
● Alias: readDomBed
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This dataExample object comprises three objects: GenomicFeatureList.GR, AnnotNames and Domains.GR. GenomicFeatureList.GR is a list of GRanges objects, one for each genomic feature to analyze. AnnotNames is a vector of the genomic feature names. Domains.GR is a GRanges object for topologically associating domains.
● Data Source:
CranContrib
● Keywords:
● Alias: dataExample
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Sexpr[results=rd,stage=build]{tools:::Rd_package_description("HiCfeat")} Author(s) Raphael Mourad
● Data Source:
CranContrib
● Keywords:
● Alias: HiCfeat, HiCfeat-package
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Function to import a genomic feature bed file. The bed file must contain coordinates of the genomic features. It can be for instance ChIP-seq peak coordinates or functional element coordinates.
● Data Source:
CranContrib
● Keywords:
● Alias: readGFBed
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