Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity


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Documentation for package ‘RgnTX’ version 1.9.0

Help Pages

calculateShift Calculate positional shifting over transcriptome
distanceTx Evaluation function
extractRegions Extract regions
getFormatCorrect getFormatCorrect
getPermSpaceByFeatures Get permutation space for features
getPermSpaceByTxID Get permutation space by specifying transcript ids
getPermSpaceByType Get permutation space by specifying type
getPvalZscore getPvalZscore
getStopCodon getStopCodon
getTransInfo Get transcript information
GRanges2GRangesList Convert a GRanges object to a GRangesList object
GRangesList2GRanges Convert a GRangesList object to a GRanges object
overlapCountsTx Evaluation function
overlapCountsTxIA Evaluation function
overlapWidthTx Evaluation function
permTestTx Perform permutation test
permTestTxIA Perform permutation test
permTestTxIA_customPick Perform permutation test
permTestTx_customAll Perform permutation test
permTestTx_customPick Perform permutation test
plotPermResults Plot permutation test results
plotShiftedZScoreTx Plot shifted z scores
randomizeFeaturesTx Randomize features into transcriptome
randomizeFeaturesTxIA Randomize features into transcriptome
randomizeTransByOrder Randomize features into transcriptome
randomizeTx Get randmized regions over transcriptome
shiftedZScoreTx Calculate shifted z scores
shiftTx Shift over transcripts
vector2GRangesList vector2GRangesList