parseCAGEscanBlocksToGrangeTSS {CAGEr} | R Documentation

## parseCAGEscanBlocksToGrangeTSS

### Description

Parse a string describing a block in a CAGEscan molecule, as output by the "CAGEscan 3.0" pipeline.

### Usage

    parseCAGEscanBlocksToGrangeTSS(blocks)

### Arguments

`blocks` | A character string representing a block in a CAGEscan molecule.

### Value

A GRanges object representing a TSS.

In CAGEscan molecules, blocks are separated by ‘|’, ‘,’ or ‘;’ for gap of coverage, splice junction (confident) and splice junction (maybe) respectively. Strand is "+" if first coordinate is lower than the second one, and "-" otherwise.

### See Also

import.CAGEscanMolecule

### Examples

    myMolecule <- paste0( "chr11:66268633-66268693,"
                        , "chr11:66271796-66271869;"
                        , "chr11:66272156-66272252|"
                        , "chr11:66272364-66272460")
    myFirstBlock <- sub("[,;|].*", "", myMolecule)

    CAGEr:::parseCAGEscanBlocksToGrangeTSS(myFirstBlock)

[Package CAGEr version 2.0.2 Index]