Platypus (version 3.6.0)

VDJ_extract_germline_consensus_ref: Making the trimmed reference and concatenating fr1-fr4

Description

Function that takes the VDJ and the fr1-fr4 sequence per antibody Based on the ref argument, if TRUE it also returns the returns in the VDJ/VJ_ref.nt/aa the trimmed reference based on the alignement with the consensus.

Usage

VDJ_extract_germline_consensus_ref(
  VDJ,
  n_clones = NA,
  samples = NA,
  ref = TRUE,
  path_toData = "../Data/"
)

Value

$vdj: VDJ containing the VDJ/VJ_ref.nt/aa columns if ref = TRUE and the full_VDJ, full_VJ columns with the fr1-fr4. $clones: clone_ids for which a reference was made.

Arguments

VDJ

VDJ or vgm[[1]] object, as obtained from the VDJ_GEX_matrix function in Platypus.

n_clones

integer, denoting the top n clones to get the reference. If NA it is performed in all clones

samples

list of sample names, with the same order as they were accessed to make the VGM

ref

bool, denoting whether or not we trim the reference of the antibodies.

path_toData

str, denoting the folder containing the VDJ folder with VDJ information per sample

Examples

# \donttest{
try({
samples = c('LCMV', 'TNFR')
vgm = read("VGM.RData")
n_clones = 20
result = VDJ_extract_germline_consensus_ref(vgm$VDJ, n_clones,
samples, ref = TRUE,
path_toData="../Data/")
VDJ = result[1]$vdj
clone_counts = result[2]$clones
})
# }