DBAmmd-class
objects.## S3 method for class 'DBAmmd':
Genome(x)## S3 method for class 'DBAmmd':
Samples(x)
## S3 method for class 'DBAmmd':
numPeaks(x)
## S3 method for class 'DBAmmd':
numSamples(x)
## S3 method for class 'DBAmmd':
metaData(x)
## S3 method for class 'DBAmmd':
Regions(x)
## S3 method for class 'DBAmmd':
Reads(x, whichPos = "Center")
## S3 method for class 'DBAmmd':
Counts(x, whichCounts = "T")
## S3 method for class 'DBAmmd':
Hists(x, whichPos = "Center")
## S3 method for class 'DBAmmd':
Dists(x, dist.method = NULL)
## S3 method for class 'DBAmmd':
Contrast(x, whichContrast = 1)
## S3 method for class 'DBAmmd':
setRegions(x, Regions)
## S3 method for class 'DBAmmd':
setContrast(x, contrast)
DBAmmd()
.
(See DBAmmd-class
for more details.)Genome(x)
returns the name of the used genome version, if set
in the metaData.Samples(x)
returns the information which was provided in the
SampleSheet.csv to describe the data.
numPeaks(x)
returns the number of Peaks / Regions of Interest
that are associated with the DBAmmd object.
numSamples(x)
returns the number of samples associated with the
DBAmmd object.
metaData(x)
returns the metaData associated with the
DBAmmd object.
Regions(x)
returns the Peaks / Regions of Interest that are
associated with the DBAmmd object.
Reads(x,whichPos)
returns the Reads mapping to the Regions of Interest.
Counts(x,whichCounts)
returns a m x n matrix containing the
Counts of Reads mapping to the Peaks / Regions of Interest.
Depending on the value of 'whichCounts', total counts ('T'),
or counts of reads mapping to positive ('p'), or negative strand ('n')
are returnt. See getPeakReads
for more details.
Hists(x,whichPos)
returns a list of matrices of length m
(number of Peaks). Each matrix is a n x L_i matrix, where n is the number of
samples and L_i is the number of bins used to cover
the extend of the peak. Note, L_i varies between peaks of different lengths.
See compHists
for more details.
Dists(x,dist.method)
returns a matrix containing distances
between pairs of samples for each peak. See compDists
for
more details.
Contrast(x,whichContrast)
returns the specified contrast.
setRegions(x,Regions)
returns a DBAmmd Object with set
Peaks / Regions of Interests.
setContrast(x,contrast)
returns a DBAmmd Object
with a set contrast.
DBAmmd-class
data("MMD")
Samples(MMD)
Genome(MMD)
numPeaks(MMD)
numSamples(MMD)
metaData(MMD)
R <- Regions(MMD)
Pos <- Reads(MMD)
C <- Counts(MMD)
H <- Hists(MMD)
D <- Dists(MMD)
C1 <- Contrast(MMD)
Run the code above in your browser using DataCamp Workspace