constructTDS {transcriptR} | R Documentation |
The function constructs an object of class TranscriptionDataSet
,
which is a container for holding processed sequencing data and the results of
all downstream analyses. All the slots of the created object are filled
during the workflow by applying specific functions to the object directly.
constructTDS(file, region, fragment.size = 250, unique = FALSE, paired.end = FALSE, swap.strand = FALSE, param = NULL)
file |
A path to a BAM file with sequencing reads. |
region |
|
fragment.size |
|
unique |
|
paired.end |
|
swap.strand |
|
param |
|
The slots fragments
, fragmentSize
, region
,
coveragePlus
, coverageMinus
are filled during the object
construction. The fragments
holds information about genomic
coordinates of the sequenced fragments (reads extended to the fragmento
size). coveragePlus
and coverageMinus
for each position in
the genome counts the number of fragments that cover it (for the details,
see coverage
). region
holds information about
the region used for fragments extraction.
An object of class TranscriptionDataSet
.
Armen R. Karapetyan
### Load TranscriptionDataSet object data(tds) ### View a short summary of the object tds