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.

Arguments

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: selection strength (Sigma), 95% confidence intervals, and P values.