map_reads: Map Reads to Reference Barcodes

In Benji-Wagner/SequenceMapper: Map Reads to Reference Barcodes

Description

map_reads is the primary workhorse of this package. It iterates through the reads_table, finds the barcodes that are within 2 Hamming distances, and then computes the probability of the read mapping to each barcode that is within 2 Hamming distances. Then, out of this list of probabilities, it selects the first barcode with the greatest probability of being a match.

Usage

map_reads(barcodes_table, reads_table, distance_threshold = 2)

Arguments

barcodes_table	The full table of reference barcodes, which contains a column titled Labels, which contains the sequence ID, and another called Code, which contains the barcode sequence.
reads_table	The full table of reads, which contains a column titled Read_ID, another called Called_Read, and a third column titled Phred_Score.
distance_threshold	Integer specifying the Hamming distance threshold for which we want to filter barcodes

Value

Returns the original reads table along with the barcode that was mapped and the probability of the map.

Examples

library(dplyr)
library(SequenceMapper)

mapped_reads <- map_reads(reads_table = reads_table, barcodes_table = barcodes_table)
mapped_reads %>% group_by(mapped_barcodes) %>%
     summarize(Number_Mapped = n(), Proportion_Mapped = n()/nrow(mapped_reads))

Benji-Wagner/SequenceMapper documentation built on June 6, 2019, 1:08 p.m.