segmentation {segmenter} | R Documentation |
The segmentation
class consists of matrices and lists. The components
contain the output of the chromatin segmentation analysis. Loading the input
data is optional. The object is returned as a result of calling
learn_model
or reading its already existing output.
model
list. The list
consists of 6 items corresponding
to the contents of the model_#.txt
file. These are
number_states
and number_marks
for the numbers of states
and marks in the model; likelihood
and probinit
for the
likelihood and the initial probabilities of the multi-state model;
transitionprobs
and emissionprobs
for the probabilities
of the transitions and emissions parameters of the model. Can be
accessed using model
.
emission
matrix. The matrix
contains the emission
parameters of n states (rows) for n marks (columns) corresponding to
the contents of the emission_#.txt
file. Can be accessed using
emission
.
transition
matrix. The matrix
contains the transition
parameters of n by n states corresponding to the contents of the
transition_#.txt
file. Can be accessed using
transition
.
overlap
list. A list
of n number of cells/conditions items.
Each item is a matrix
of the overlap enrichment of n states
(rows) at n genomic annotations (columns) corresponding to the contents
of the <cell>_#_overlap.txt
files. Can be accessed using
overlap
.
TSS
list. A list
of n number of cells/conditions items.
Each item is a matrix
of the overlap enrichment of n states
(rows) at n locations around the transcription start site (TSS)
(columns) corresponding to the contents of the
<cell>_#_TSS_neighborhood.txt
files. Can be accessed using
TSS
.
TES
list. A list
of n number of cells/conditions items.
Each item is a matrix
of the overlap enrichment of n states
(rows) at n locations around the transcription end site (TES)
(columns) corresponding to the contents of the
<cell>_#_TES_neighborhood.txt
files. Can be accessed using
TES
.
segment
list. A list
of n number of cells/conditions items.
Each item is a GRanges
object containing the
segmentation and assigned states as a metadata column 'state'. These
contents correspond to the <cell>_#_segment.bed
files. Annotations
of the ranges are optional. Can be accessed using segment
.
bins
list. A list
of n number of cells/conditions items.
Each item is a SummarizedExperiment
object containing the binarized input data. The coordinates of the bins
are saved as the rowRanges
each
assigned to a state and the binary data itself is saved as
assay
. Can be accessed using
bins
.
counts
list. A list
of n number of cells/conditions items.
Each item is a SummarizedExperiment
object containing the read counts in bins. The coordinates of the bins
are saved as the rowRanges
each
assigned to a state and the counts data itself is saved as
assay
. Can be accessed using
counts
.