createGermlines

createGermlines - createGermlines Determine consensus clone sequence and create germline for clone

Description¶

createGermlines Determine consensus clone sequence and create germline for clone

Usage¶

createGermlines(
data,
references,
locus = "locus",
nproc = 1,
seq = "sequence_alignment",
v_call = "v_call",
d_call = "d_call",
j_call = "j_call",
amino_acid = FALSE,
id = "sequence_id",
clone = "clone_id",
v_germ_start = "v_germline_start",
v_germ_end = "v_germline_end",
v_germ_length = "v_germline_length",
d_germ_start = "d_germline_start",
d_germ_end = "d_germline_end",
d_germ_length = "d_germline_length",
j_germ_start = "j_germline_start",
j_germ_end = "j_germline_end",
j_germ_length = "j_germline_length",
np1_length = "np1_length",
np2_length = "np2_length",
na.rm = TRUE,
fields = NULL,
verbose = 0,
...
)

Arguments¶

data: AIRR-table containing sequences from one clone
references: Full list of reference segments, see readIMGT
locus: Name of the locus column in the input data
nproc: Number of cores to use
seq: Column name for sequence alignment
v_call: Column name for V gene segment gene call
d_call: Column name for D gene segment gene call
j_call: Column name for J gene segment gene call
amino_acid: Perform reconstruction on amino acid sequence (experimental)
id: Column name for sequence ID
clone: Column name for clone ID
v_germ_start: Column name of index of V segment start within germline
v_germ_end: Column name of index of V segment end within germline
v_germ_length: Column name of index of V segment length within germline
d_germ_start: Column name of index of D segment start within germline
d_germ_end: Column name of index of D segment end within germline
d_germ_length: Column name of index of D segment length within germline
j_germ_start: Column name of index of J segment start within germline
j_germ_end: Column name of index of J segment end within germline
j_germ_length: Column name of index of J segment length within germline
np1_length: Column name in receptor specifying np1 segment length
np2_length: Column name in receptor specifying np2 segment length
na.rm: Remove clones with failed germline reconstruction?
fields: Character vector of additional columns to use for grouping. Sequences with disjoint values in the specified fields will be considered as separate clones.
verbose: amount of rubbish to print
…: Additional arguments passed to buildGermline

Value¶

Tibble with reconstructed germlines

Details¶

Return object adds/edits following columns:

seq: Sequences potentially padded same length as germline
germline_alignment: Full length germline
germline_alignment_d_mask: Full length, D region masked
vonly: V gene segment of germline if vonly=TRUE
regions: String of VDJ segment in position if use_regions=TRUE

Examples¶

vdj_dir <- system.file("extdata", "germlines", "imgt", "human", "vdj", package="dowser")
imgt <- readIMGT(vdj_dir)

[1] "Read in 3 from 3 fasta files"

db <- createGermlines(ExampleAirr[1,], imgt)

Warning:locus column not found, attempting to extract locus from V callWarning:Loci found: IGHWarning:Allele IGHV3-4903 is not in the provided germline database.Warning:Allele IGHD6-1301 is not in the provided germline database.Warning:Removing 1 failed clonal germlines. Clones: 3128