Skip to contents

Common sequences in two or more repertoire_ids

Source: R/commonSeqs.R
commonSeqs.Rd

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
)
#> # A tibble: 1 × 3
#>   junction_aa     TRB_Unsorted_0 TRB_Unsorted_32
#>   <chr>                    <dbl>           <dbl>
#> 1 CASSQDRTGQYGYTF        0.00429          0.0152