README.md

In teasdalm/rmindex: R codex to look a multiplex indexes

rmindex

rmindex (R Meyer index) is an R package that assesses and selects multiplex indexes from the Meyer and Kircher (2010) library protocol for use with illumina sequencing.

Usage

• install rmindex

install.packages("devtools")
install.packages("tidyr")
devtools::install_github("teasdalm/rmindex")
library(rmindex)

• Read barcodes and plot

# Read barcodes
# Example file in /data
barcode_df <- read_index("barcodes.csv")

# Plot barcodes
plot_barcodes(barcode_df)

# All in one
plot_barcodes(read_index("barcodes.csv"))

• Select random none overlaping indexes

# Select random barcodes defaults are shown
barcode_select(number_to_select = 6)

# example output 
# Selected indexes B023 B029 B033 B039 B040 B046
#   TCD_name     Seq base1 base2 base3 base4 base5 base6 base7
#23     B023 GATCTCG     G     A     T     C     T     C     G
#29     B029 CCGATTG     C     C     G     A     T     T     G
#33     B033 CATCCGG     C     A     T     C     C     G     G
#39     B039 CGAATGC     C     G     A     A     T     G     C
#40     B040 TTCGCAA     T     T     C     G     C     A     A
#46     B046 GTACCGG     G     T     A     C     C     G     G

# Select and plot
plot_barcodes(barcode_select(number_to_select = 6))

• with more complex indexes

# Select random barcodes 
barcode_select(indexes = c(1,4,63:100), number_to_select = 6)

# example output 
#selected indexes B072 B085 B086 B087 B088 B093
#   TCD_name     Seq base1 base2 base3 base4 base5 base6 base7
#72     B072 GGCATAG     G     G     C     A     T     A     G
#85     B085 CCGGATA     C     C     G     G     A     T     A
#86     B086 GCCGCCT     G     C     C     G     C     C     T
#87     B087 AACGACC     A     A     C     G     A     C     C
#88     B088 CCAGCGG     C     C     A     G     C     G     G
#93     B093 GACTTCT     G     A     C     T     T     C     T

• MiSeq sample sheet test

sample_sheet_test("sample_sheet.csv")

Data

• Data folder includes...
• index.rda - 200 plus Meyer and Kircher (2010) indexes

• example_barcodes.csv - example index csv file

• To load meyer index dataset

library(rmindex)
head(meyer_index)

teasdalm/rmindex documentation built on Feb. 28, 2023, 5:08 a.m.