commonSeqs: Common sequences in two or more repertoire_ids

In elulu3/LymphoSeqTest: 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 LymphoSeq function productiveSeq where aggregate = "junction_aa".
repertoire_ids	A character vector of two or more repertoire_id names in productive.aa.

Value

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

See Also

commonSeqsVenn commonSeqsPlot commonSeqsBar

Examples

file_path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq2")

stable <- readImmunoSeq(path = file_path)

atable <- productiveSeq(study_table = stable, aggregate = "junction_aa")

commonSeqs(repertoire_ids = c("TRB_Unsorted_0", "TRB_Unsorted_32"),
   study_table = atable)

elulu3/LymphoSeqTest documentation built on Aug. 27, 2022, 5:47 a.m.