Baseline-class - S4 class defining a BASELINe (selection) object
Description¶
Baseline
defines a common data structure the results of selection
analysis using the BASELINe method.
Usage¶
"plot"(x, y, ...)
"summary"(object, nproc = 1)
Arguments¶
- x
Baseline
object.- y
- name of the column in the
db
slot ofbaseline
containing primary identifiers. - …
- arguments to pass to plotBaselineDensity.
- object
Baseline
object.- nproc
- number of cores to distribute the operation over.
Slots¶
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 dimensionsr 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 dimensionsr 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 dimensionsr 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 dimensionsr 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
andfwr
). Matrices have dimensionsr 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 also¶
See summarizeBaseline for more information on @stats
.