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Frequency table

Source: R/barcode_frequency.R
create_freq_table.Rd

Creates a sorted frequency table of each of the observed barcode combinations. This function is indended to be used after running filter_demultiplex_res() and before creating frequency plots, knee plots, or selecting the number of barcodes to include.

Usage

create_freq_table(assigned_barcodes)

Arguments

assigned_barcodes

A character or integer matrix, corresponding to the field assigned_barcodes from combinatorial_demultiplex() or the field demultiplex_res$assigned_barcodes from filter_demultiplex_res().

Value

A data frame where each row corresponds to a unique observed barcode combination. The rows are sorted in descending order of frequency. The first columns specify the barcode assignment (e.g bc3, bc2, bc1) and the last columns were the following:

  • frequency: The number of reads with the barcode combination.

  • cumulative_frequency: The cumulative frequency of the barcode combination counted from the top.

  • fraction: The fraction of reads with the barcode combination.

  • cumulative_fraction: The cumulative fraction of the barcode combination counted from the top.

Examples

library(purrr)
library(Biostrings)
input_fastq <- system.file(
    "extdata", "PETRI-seq_forward_reads.fq.gz", package = "posDemux")
reads <- readDNAStringSet(input_fastq, format = "fastq")
barcode_files <- system.file(
    "extdata/PETRI-seq_barcodes",
    c(bc1 = "bc1.fa", bc2 = "bc2.fa", bc3 = "bc3.fa"),
    package = "posDemux"
    )
names(barcode_files) <- paste0("bc", 1L:3L)
barcode_index <- map(barcode_files, readDNAStringSet)
barcodes <- barcode_index[c("bc3", "bc2", "bc1")]
sequence_annotation <- c(UMI = "P", "B", "A", "B", "A", "B", "A")
segment_lengths <- c(7L, 7L, 15L, 7L, 14L, 7L, NA_integer_)
demultiplex_res <- posDemux::combinatorial_demultiplex(
    reads, barcodes = barcodes, segments = sequence_annotation,
    segment_lengths = segment_lengths
    )
filtered_res <- filter_demultiplex_res(demultiplex_res, allowed_mismatches = 1L)
freq_table <- create_freq_table(filtered_res$demultiplex_res$assigned_barcodes)