AntibodyForests (version 1.1.0)

Af_PLM_dataframe: 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)

Value

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

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.

Examples

if (FALSE) {
PLM_dataframe <- Af_PLM_dataframe(AntibodyForests_object = AntibodyForests::small_af,
                 sequence.name = "VDJ_sequence_aa_trimmed",
                 path_to_probabilities = "/directory/ProbabilityMatrix")
}