Man pages for FabianErdel/RWire
Identification of co-regulated genomic regions based on correlation analysis

AccMatrix-classAccMatrix class that is used to store accessibility matrices
compareCorCoeffsThis function returns p-values assessing the difference...
compareCorDistributionsThis function returns p-values assessing the difference...
CorMatrix-classCorMatrix class that is used to store correlation matrices
countReadsThis function counts reads in a GRanges object that fall into...
cropAccMatrixThis function crops accessibility matrices
cropCorMatrixThis function crops correlation matrices
getAccLUTThis function makes a color LUT for accessibility matrices
getCIsThis function returns confidence intervals
getCorBackgroundThis function returns the background correlation obtained...
getCorLUTThis function makes a color LUT for correlation matrices
getCorRangesThis function returns bootstrapped correlation coefficients
getPEPairsThis function returns promoter-enhancer (P-E) pairs based on...
makeAccMatrixThis function makes accessibility matrices from a set of BED...
makeCorMatrixThis function makes a correlation matrix from two...
makeGenomeTilesThis function makes tiles for the complete hg19 genome
makeIPCHistThis function makes a histogram for the number of...
makeIPCStatsCalculate statistics for the number of integrations per cell
makeIPRHistThis function makes a histogram for the number of cells with...
makeIPRStatsCalculate statistics for the number of integrations per ROI
makeTilesThis function makes tiles for a particular chromosome of the...
PEPairs-classPEPairs class that is used to store sets of promoter-enhancer...
readBedThis function reads a BED file and stores the reads in a...
removeEmptyRowsThis function removes empty rows from accessibility matrices
removeRowsBelowCutoffThis function removes rows below a certain cutoff from...
saveImageThis function saves a matrix as an image
scaleAccMatrixThis function scales accessibility matrices to genomic...
scaleCorMatrixThis function scales correlation matrices to genomic...
writeMatrixWrapper for making and storing scaled corrleation matrices...
FabianErdel/RWire documentation built on Oct. 3, 2018, 11:28 p.m.