seqMatrix: Sequence matrix

In shashidhar22/LymphoSeq2: Analyze high-throughput sequencing of T and B cell receptors

Sequence matrix

Description

Creates a data frame with unique, productive amino acid sequences as rows and repertoire_id names as headers. Each value in the data frame represents the frequency that the sequence appeared in the repertoire_id.

Usage

seqMatrix(amino_table, sequences = NULL, by = "duplicate_frequency")

Arguments

amino_table	A tibble of productive amino acid sequences generated by LymphoSeq2 function productiveSeq() where the aggregate parameter was set to"junction_aa".
sequences	A character vector of amino acid sequences of interest. It is useful to specify the output from the LymphoSeq functions uniqueSeqs() or topSeqs() and sub-setting the "junction_aa" column. See examples below.
by	Available options are "duplicate_frequency" and "duplicate_count". Default is "duplicate_frequency".

Value

Returns a data frame of unique, productive amino acid sequences as rows and the \

See Also

topSeqs() and uniqueSeqs()

Examples

file_path <- system.file("extdata", "TCRB_sequencing",
 package = "LymphoSeq2")
study_table <- LymphoSeq2::readImmunoSeq(path = file_path, threads = 1)
study_table <- LymphoSeq2::topSeqs(study_table, top = 100)
amino_table <- LymphoSeq2::productiveSeq(study_table,
  aggregate = "junction_aa"
)
top_seqs <- LymphoSeq2::topSeqs(amino_table,
  top = 1
)
sequence_matrix <- LymphoSeq2::seqMatrix(amino_table,
  sequences = top_seqs$junction_aa, by = "duplicate_frequency"
)
unique_seqs <- LymphoSeq2::uniqueSeqs(amino_table)
sequence_matrix <- LymphoSeq2::seqMatrix(amino_table,
  sequences = unique_seqs$junction_aa, by = "duplicate_frequency"
)
# It can be helpful to combine top.freq and sequence.matrix
top_freq <- LymphoSeq2::topFreq(amino_table, frequency = 0.001)
sequence_matrix <- LymphoSeq2::seqMatrix(amino_table,
 sequences = top_freq$junction_aa)
top_freq_matrix <- merge(top_freq, sequence_matrix)

shashidhar22/LymphoSeq2 documentation built on Jan. 16, 2024, 4:29 a.m.