Man pages for ibn-salem/genepair
Functions to Analyse Pairs of Genomic Elements like Genes.

addCorAdds Pearson correlation coefficient for all gene pairs
addGeneAnnotationAdd annotatino column of each gene to gene pairs
addPairDistAdd linear distance between gene paires or NA if on differnet...
addPairExpAdds the expression values for both genes
addSameStrandAdd same starnd information.
addSubTADmodeAdd column to indicate that two query region overlap the same...
addWithinSubjectAdd column to indicate that query lies within at least one...
applyToCisPairsApply a function to a pair of genomic ranges.
applyToClosePairsApply a function to pairs of close genomic regions.
containsGenePairsTest if gene pairs are contained in another set of gene...
filterForCisPairsGet subset of gene pairs that are located on the same...
genepairgenepair: Functions to Analyse Pairs of Genomic Elements like...
getAllCisPairsGet all possible gene pairs within a given distance range as...
getCorReturns the Pearson correlation coefficient for expression of...
getPairAsGRMake GRange object of range between start position of paired...
getPairAsGRLMake GRangesList object of range between start position of...
getPairIDCreates an ID for each gene pair by concatenating both gene...
getPairIDsortedReturns a unique gene ID for each pair that is independent of...
getRandomPairsSample randomly pairs from set of genes with equal...
interChromPairMatrixInter-chromosomal gene pairs counts matrix
nonOverlappingGenePairsTest if gene pairs are non-overlapping. That is that two...
noZeroVarreturns indecies of columns with non-zero variance
pairNotNAChecks that none of the genes in pairs is NA.
percentIncludedReturns the percentage of gene pairs that are contained in...
samplePairsByWeightSample pairs from the input gene pairs according to given...
uniquePairRemove duplicated entries of gene pairs of the form A-B and...
uniquePairPerGeneGet only one pair per unique gene.
uniquePairPerGeneBySimGet only one pair per unique gene by choosing the gene pair...
weightsByBinCompute sampling weights for continues values by binning.
weightsByFactorFreqCompute sampling weights for descret values.
ibn-salem/genepair documentation built on Aug. 7, 2017, 9:47 a.m.