SPANTCR: Analyze a TCR Set

In alexandermxu/SPANTCR: Analyzes TCR Datasets

Description

Take a set of TCR CDR3s and process into a CDR3Breakdown object

Usage

SPANTCR(
  Data,
  Filename,
  FileType,
  AAOperation = "Hydrophobicity",
  TickNumber = 100,
  SlidingWindowTickSize = 2,
  SignificanceCutoff = 0.03,
  ScoreFunction = ScoreFunctionExponential5,
  WeightFunction = WeightFunctionLinear
)

Arguments

Data	Datatable with columns CDR3/vgene/jgene/gene/score/id (if paired). Column gene has values "TCRA" or "TCRB". Column id has matched numbers for paired TCRA/B genes.
Filename	Name of file or data
FileType	"Paired" "TCRA" or "TCRB"
AAOperation	Column to use from object AminoAcidFilter
TickNumber	Number of bins to use, default 100
SlidingWindowTickSize	k-mer length, 1/2/3 allowed currently, default 2
SignificanceCutoff	Minimum proportion of k-mers present in each bin to be displayed, default 0.03
ScoreFunction	How to prioritize internal scoring of TCRs, default 5^score
WeightFunction	How to weight the influence of each k-mer, default linear growth/decay

Value

CDR3Breakdown object, data table of CDR3 composition in bins

Examples

SPANTCR(VDJDBCMVPairedInput, "VDJDBCMV", "Paired", "Hydrophobicity", 100, 2,
0.03, ScoreFunctionExponential5, WeightFunctionLinear)
SPANTCR(VDJDBCMVPairedInput[gene=="TRA"], "VDJDBCMVAlpha","TRA","Mass", 100,
2, 0.05, ScoreFunctionExponential5, WeightFunctionLinear)

alexandermxu/SPANTCR documentation built on Dec. 19, 2021, 12:30 a.m.