TranscriptionDataSet-class {transcriptR} | R Documentation |
The TranscriptionDataSet
is a S4 class to store input values,
intermediate calculations and results of the transcripts detection and
quantification analysis.
bamFile
Character
. Path to a BAM file.
fragments
GRanges
. Sequencing reads
extended to the fragment size.
fragmentSize
Numeric
. Fragment size in base pairs (bp).
region
GRanges
. Genomic region(s) to
extract reads from.
coveragePlus
RleList
. Fragment coverage profile
for the forward DNA strand.
coverageMinus
RleList
. Fragment coverage profile
for the reverse DNA strand.
coverageCutoff
Numeric
. Background coverage cutoff value.
coverageCutoffFdr
Numeric
. False Discovery Rate (FDR) used to
estimate background coverage cutoff.
gapDistanceTest
Data.Frame
. Tested gap distances and
corresponding error rates.
gapDistanceTestCovCutoff
Numeric
. Coverage cutoff value used for
the gap distance estimation.
transcripts
GRanges
. Identified transcripts.
transcriptsCovCutoff
Numeric
. Coverage cutoff value used for the
transcripts detection.
transcriptsGapDist
Numeric
. Gap distance value used for the
transcripts detection.
transcriptsNormalization
Numeric
. Total number of reads used for
normalization when calculating FPKM.
Armen R. Karapetyan