beta.prob: List with assembling probabilities of beta chain TCRs.

In tcR: Advanced Data Analysis of Immune Receptor Repertoires

Description

beta.prob is a list with probabilities of TCR assembling taken from Murugan et al. Statistical inference of the generation probability of T-cell receptors from sequence repertoires. It's a list with the following elements:

- P.V - matrix with 1 column and row names stands for V-beta segments. Each element is a probability of choosing corresponding V-beta segment.

- P.del.D1 - matrix 17x17 with probabilities of choosing D5-D3 deletions for TRBD1.

- P.del.D1 - matrix 17x17 with probabilities of choosing D5-D3 deletions for TRBD2.

- P.ins.len - matrix with first columns stands for number of insertions, second and third columns filled with probability values of choosing corresponding number of insertions in VD- and DJ-junctions correspondingly.

- P.ins.nucl - data frame with probability of choosing a nucleotide in the insertion on junctions with known previous nucleotide. First column with names of nucleotides, 2-5 columns are probabilities of choosing adjacent nucleotide in VD-junction, 6-9 columns are probabilities of choosing adjacent nucleotide in DJ-junction.

- P.del.J - matrix with the first column "P.del.V" with number of deletions, and other columns with names for V-segments and with probabilities of corresponding deletions.

- P.del.J - matrix with the first column "P.del.J" with number of deletions, and other columns with names for J-segments and with probabilities of corresponding deletions.

- P.J.D - matrix with two columns ("TRBD1" and "TRBD2") and 13 rows with row names stands for J-beta segments. Each element is a mutual probability of choosing J-D segments.

Format

beta.prob is a list of matrices and data frames.

Examples

## Not run: 
# Generate 10 kmers with adjacent nucleotide probability.
generate.kmers.prob(rep.int(10, 10), .probs=beta.prob$P.ins.nucl[,c(1, 2:5)])

## End(Not run)

tcR documentation built on July 2, 2020, 3:18 a.m.