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

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

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