findConsensusSequences: Find consensus sequences Find consensus sequences within EOS...

In AdaptiveCompBio/EOS: Commonly used functions for the EOS project

Description

Find consensus sequences Find consensus sequences within EOS report(s)

Usage

findConsensusSequences(..., report_list = NULL, no_shm_allowance = T,
  max_adj_mut_igkl = 0, max_adj_mut_igh = 2, ndn_cost = 1.05)

Arguments

...	Any number of EOS report objects
report_list	A list of EOS report objects
no_shm_allowance	Should mutations be allowed?
max_adj_mut_igkl	If the EOS report query doesn't have a pre-specified max adjusted mutation value for a sequence, use this default for IGKL sequences
max_adj_mut_igh	If the EOS report query doesn't have a pre-specified max adjusted mutation value for a sequence, use this default for IGH/IGH_D sequences
ndn_cost	Modified cost for an ndn base pair mismatch

Value

A list with S3 class "Consensus_List". Each element in the list is a vector of matching sequences and corresponding locus in the "locus" attribute field. The names of the list correspond to the dominant sequence of the consensus cluster (i.e., the shortest).

AdaptiveCompBio/EOS documentation built on May 26, 2019, 6:37 a.m.