removeSeq: Remove sequence

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

Remove sequence

Description

Removes an amino acid sequence and associated data from all instances within study table and then recomputes the duplicate_frequency.

Usage

removeSeq(study_table, sequence)

Arguments

study_table	A tibble imported using the LymphoSeq2 function readImmunoSeq(). "junction_aa", "duplicate_count", and "duplicate_frequency" are required columns.
sequence	A character vector of one or more amino acid sequences to remove from the study table

Value

Returns a tibble like the one imported except all rows with the specified amino acid sequence are removed. The "duplicate_frequency" is recalculated.

Examples

file_path <- system.file("extdata", "TCRB_sequencing",
 package = "LymphoSeq2")
study_table <- LymphoSeq2::readImmunoSeq(path = file_path, threads = 1)
Lstudy_table <- LymphoSeq2::topSeqs(study_table, top = 100)
LymphoSeq2::searchSeq(study_table, sequence = "CASSDLIGNGKLFF")
cleaned_table <- LymphoSeq2::removeSeq(study_table,
 sequence = "CASSDLIGNGKLFF")
LymphoSeq2::searchSeq(cleaned_table, sequence = "CASSDLIGNGKLFF")

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