createGermlines {dowser}

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

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

Value

Tibble with reconstructed germlines

See Also

createGermlines buildGermline, stitchVDJ

Examples

vdj_dir <- system.file("extdata", "germlines", "imgt", "human", "vdj", package="dowser")
imgt <- readIMGT(vdj_dir)
db <- createGermlines(ExampleAirr[1,], imgt)