parseCAGEscanBlocksToGrangeTSS: parseCAGEscanBlocksToGrangeTSS

In charles-plessy/CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

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)

charles-plessy/CAGEr documentation built on Oct. 27, 2024, 10:11 p.m.