findNovelAlleles - Find novel alleles from repertoire sequencing data
findNovelAlleles analyzes mutation patterns in sequences thought to
align to each germline allele in order to determine which positions
might be polymorphic.
findNovelAlleles(clip_db, germline_db, germline_min = 200, min_seqs = 50, auto_mutrange = TRUE, mut_range = 1:10, pos_range = 1:312, y_intercept = 0.125, alpha = 0.05, j_max = 0.15, min_frac = 0.75, nproc = 1)
data.framein Change-O format. See details.
- a vector of named nucleotide germline sequences
matching the V calls in
- the minimum number of sequences that must have a particular germline allele call for the allele to be analyzed
- the minimum number of total sequences (within the desired mutational range and nucleotide range) required for the samples to be considered
TRUE, the algorithm will attempt to determine the appropriate mutation range automatically using the mutation count of the most common sequence assigned to each allele analyzed
- the range of mutations that samples may carry and be considered by the algorithm
- the range of IMGT-numbered positions that should be considered by the algorithm
- the y-intercept above which positions should be considered potentially polymorphic
- the alpha cutoff to be used when constructing the confidence interval for the y-intercept
- the maximum fraction of sequences perfectly aligning to a potential novel allele that are allowed to utilize to a particular combination of junction length and J gene
- the minimum fraction of sequences that must have usable nucleotides in a given position for that position to considered
- the number of processors to use
data.frame with a row for each known allele analyzed.
Besides metadata on the the parameters used in the search, each row will have
either a note as to where the polymorphism-finding algorithm exited or a
nucleotide sequence for the predicted novel allele.
data.frame in Change-O format contains the following
"SEQUENCE_IMGT"containing the IMGT-gapped nucleotide sequence
"V_CALL"containing the IMGT/V-QUEST V allele call(s)
"J_CALL"containing the IMGT/V-QUEST J allele call(s)
"JUNCTION_LENGTH"containing the junction length
The TIgGER allele-finding algorithm, briefly, works as follows: Mutations are determined through comparison to the provided germline. Mutation frequency at each position is determined as a function of sequence-wide mutation counts. Polymorphic positions exhibit a high mutation frequency despite sequence-wide mutation count. False positive of potential novel alleles resulting from clonally-related sequences are guarded against by ensuring that sequences perfectly matching the potential novel allele utilize a wide range of combinations of J gene and junction length.
# Load example data and germlines data(sample_db) data(germline_ighv) # Find novel alleles and return relevant data ### Not run: novel_df = findNovelAlleles(sample_db, germline_ighv)
plotNovel to visualize the data supporting any novel alleles hypothesized to be present in the data and inferGenotype to determine if the novel alleles are frequent enought to be included in the subject’s genotype