shazam (version 1.3.0)

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

# S4 method for Baseline,character
plot(x, y, ...)
# S4 method for Baseline
summary(object, nproc = 1)

Arguments

x

Baseline object.

y

name of the column in the db slot of baseline 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 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 dimensions, 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.