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.

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 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.