inferGenotype {tigger} | R Documentation |
Infer a subject-specific genotype using a frequency method
Description
inferGenotype
infers an subject's genotype using a frequency method.
The genotype is inferred by finding the minimum number set of alleles that
can explain the majority of each gene's calls. The most common allele of
each gene is included in the genotype first, and the next most common allele
is added until the desired fraction of alleles can be explained. In this
way, mistaken allele calls (resulting from sequences which
by chance have been mutated to look like another allele) can be removed.
Usage
inferGenotype(
data,
germline_db = NA,
novel = NA,
v_call = "v_call",
seq = "sequence_alignment",
fraction_to_explain = 0.875,
gene_cutoff = 1e-04,
find_unmutated = TRUE
)
Arguments
data |
|
germline_db |
named vector of sequences containing the
germline sequences named in
|
novel |
optional |
v_call |
column in |
seq |
name of the column in |
fraction_to_explain |
the portion of each gene that must be explained by the alleles that will be included in the genotype. |
gene_cutoff |
either a number of sequences or a fraction of
the length of |
find_unmutated |
if |
Details
Allele calls representing cases where multiple alleles have been
assigned to a single sample sequence are rare among unmutated
sequences but may result if nucleotides for certain positions are
not available. Calls containing multiple alleles are treated as
belonging to all groups. If novel
is provided, all
sequences that are assigned to the same starting allele as any
novel germline allele will have the novel germline allele appended
to their assignent prior to searching for unmutated sequences.
Value
A data.frame
of alleles denoting the genotype of the subject containing
the following columns:
-
gene
: The gene name without allele. -
alleles
: Comma separated list of alleles for the givengene
. -
counts
: Comma separated list of observed sequences for each corresponding allele in thealleles
list. -
total
: The total count of observed sequences for the givengene
. -
note
: Any comments on the inferrence.
Note
This method works best with data derived from blood, where a large portion of sequences are expected to be unmutated. Ideally, there should be hundreds of allele calls per gene in the input.
See Also
plotGenotype for a colorful visualization and genotypeFasta to convert the genotype to nucleotide sequences. See inferGenotypeBayesian to infer a subject-specific genotype using a Bayesian approach.
Examples
# Infer IGHV genotype, using only unmutated sequences, including novel alleles
inferGenotype(AIRRDb, germline_db=SampleGermlineIGHV, novel=SampleNovel,
find_unmutated=TRUE)