Af_PLM_dataframe: Function to create a dataframe of the Protein Language Model...

In AntibodyForests: Delineating Inter- And Intra-Antibody Repertoire Evolution

Function to create a dataframe of the Protein Language Model probabilities and ranks of the mutations along the edges of B cell lineage trees.

Description

Function to create a dataframe of the Protein Language Model probabilities and ranks of the mutations along the edges of B cell lineage trees.

Usage

Af_PLM_dataframe(AntibodyForests_object, sequence.name, path_to_probabilities)

Arguments

AntibodyForests_object	AntibodyForests-object, output from Af_build()
sequence.name	character, name of the sequence column in the AntibodyForests object (example VDJ_sequence_aa_trimmed)
path_to_probabilities	character, path to the folder containing probability matrices for all sequences. Probability matrices should be in CSV format and the filename should include sampleID_clonotypeID_nodeNR, matching the AntibodyForests-object.

Value

A dataframe with the sample, clonotype, node numbers, number of substitutions, mean substitution rank and mean substitution probability

Examples

## Not run: 
PLM_dataframe <- Af_PLM_dataframe(AntibodyForests_object = AntibodyForests::small_af,
                 sequence.name = "VDJ_sequence_aa_trimmed",
                 path_to_probabilities = "/directory/ProbabilityMatrix")

## End(Not run)

AntibodyForests documentation built on April 4, 2025, 4:45 a.m.