An R package to associate peaks and target genes

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Documentation for package ‘Site2Target’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

addColumn2geneWiseAssociation	Add column to gene-wise association
addRelation2geneWiseAssociation	Add a relation column to gene-peak interaction table
data	MEIS cardiomyocytes datasets used in the package
extendSitesInGivenRegions	Extend sites given regions boundaries
genewiseAssociation	Generate genewise association between genes and peaks
getCenterOfPeaks	Return center of the given granges files
getNameFromCoordinates	Get names of genes or peaks related to a query coordinates
getTargetGenesNumber	generate number of sites per gene given distances
getTargetGenesPvals	Fit Negative binomial distribution to target genes
getTargetGenesPvalsWithDNAInteractions	Fit Negative binomial distribution to target genes
getTargetGenesPvalsWithIntensities	Fit log-normal distribution to target genes
getTargetGenesPvalsWithIntensitiesAndDNAInteractions	Fit log-normal distribution to target genes
granges2String	Convert granges to strings of coordinates
removeReserveCharacter	Remove reserved characters from a string
site2GeneDistance	Return the distance between paired peaks and genes
Site2Target	Associate peaks and target genes
string2Granges	Convert strings to granges of coordinates
Table2Granges	Take Genomic Ranges from a table file