parseCAGEscanBlocksToGrangeTSS {CAGEr} | R Documentation |
Parse a string describing a block in a CAGEscan molecule, as output by the "CAGEscan 3.0" pipeline.
parseCAGEscanBlocksToGrangeTSS(blocks)
blocks |
A character string representing a block in a CAGEscan molecule. |
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.
import.CAGEscanMolecule
myMolecule <- paste0( "chr11:66268633-66268693," , "chr11:66271796-66271869;" , "chr11:66272156-66272252|" , "chr11:66272364-66272460") myFirstBlock <- sub("[,;|].*", "", myMolecule) CAGEr:::parseCAGEscanBlocksToGrangeTSS(myFirstBlock)