Baseline-class | R Documentation |
Baseline
defines a common data structure the results of selection
analysis using the BASELINe method.
## S4 method for signature 'Baseline,character'
plot(x, y, ...)
## S4 method for signature 'Baseline'
summary(object, nproc = 1)
x |
|
y |
name of the column in the |
... |
arguments to pass to plotBaselineDensity. |
object |
|
nproc |
number of cores to distribute the operation over. |
description
character
providing general information regarding the
sequences, selection analysis and/or object.
db
data.frame
containing annotation information about
the sequences and selection results.
regionDefinition
RegionDefinition object defining the regions and boundaries of the Ig sequences.
testStatistic
character
indicating the statistical framework
used to test for selection. For example, "local"
or
"focused"
.
regions
character
vector defining the regions the BASELINe
analysis was carried out on. For "cdr"
and "fwr"
or "cdr1"
, "cdr2"
, "cdr3"
, etc.
numbOfSeqs
matrix
of dimensions r x c
containing the number of
sequences or PDFs in each region, where:
r
= number of rows = number of groups or sequences.
c
= number of columns = number of regions.
binomK
matrix
of dimensions r x c
containing the number of
successes in the binomial trials in each region, where:
r
= number of rows = number of groups or sequences.
c
= number of columns = number of regions.
binomN
matrix
of dimensions r x c
containing the total
number of trials in the binomial in each region, where:
r
= number of rows = number of groups or sequences.
c
= number of columns = number of regions.
binomP
matrix
of dimensions r x c
containing the probability
of success in one binomial trial in each region, where:
r
= number of rows = number of groups or sequences.
c
= number of columns = number of regions.
pdfs
list
of matrices containing PDFs with one item for each
defined region (e.g. cdr
and fwr
). Matrices have dimensions
r x c
dementions, where:
r
= number of rows = number of sequences or groups.
c
= number of columns = length of the PDF (default 4001).
stats
data.frame
of BASELINe statistics,
including: mean selection strength (mean Sigma), 95% confidence
intervals, and p-values with positive signs for the presence of
positive selection and/or p-values with negative signs for the
presence of negative selection.
See summarizeBaseline for more information on @stats
.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.