loadFileIntoGPos {CAGEr} | R Documentation |
A private (non-exported) function to load from each file format supported by CAGEr
loadFileIntoGPos(filepath, filetype = c("bam", "bamPairedEnd", "bed", "bedctss", "bedScore", "CAGEscanMolecule", "ctss"), sequencingQualityThreshold, mappingQualityThreshold, removeFirstG, correctSystematicG, genome)
filepath |
The path to the file to load. |
filetype |
The type of the file |
sequencingQualityThreshold |
See getCTSS(). |
mappingQualityThreshold |
See getCTSS(). |
removeFirstG |
See getCTSS(). |
correctSystematicG |
See getCTSS(). |
genome |
See coerceInBSgenome(). |
A GPos()
object where the score represents the number of CAGE tags
starting on that nucleotide.
import.CTSS
Other loadFileIntoGPos: bam2CTSS
,
import.CTSS
, import.bam.ctss
,
import.bam
, import.bedCTSS
,
import.bedScore
,
import.bedmolecule
,
moleculesGR2CTSS