commonSeqs: Common sequences in two or more repertoire_ids

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

Common sequences in two or more repertoire_ids

Description

Creates a data frame of the common sequences in two or more repertoire_ids, reporting their frequencies in each.

Usage

commonSeqs(study_table, repertoire_ids = NULL)

Arguments

study_table	A list of productive amino acid sequences generated by the LymphoSeq2 function productiveSeq() where aggregate = "junction_aa".
repertoire_ids	A character vector of two or more repertoire_id names in study_table.

Value

Returns a data frame of the common sequences between two or more files displaying their frequencies in each.

See Also

productiveSeq(), commonSeqsVenn(), commonSeqsPlot(), commonSeqsBar()

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 = study_table,
  aggregate = "junction_aa"
)
LymphoSeq2::commonSeqs(
  repertoire_ids = c("TRB_Unsorted_0", "TRB_Unsorted_32"),
  study_table = amino_table
)

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