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

## Documentation for package ‘RgnTX’ version 1.4.0

- 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