In LucasFVoges/GRADA: NGS data sequence (adapter) analyser

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Setup:

library(GRADA)
library(parallel)
library(DT)
library(rmarkdown)

Example Data:

# The example data from Phage - SRX6454172 (first 100 reads) can be used to test the function.
read1 <- system.file("extdata", "grada_R1.fastq", package = "GRADA")
read2 <- system.file("extdata", "grada_R2.fastq", package = "GRADA")
seq <- system.file("extdata", "adapter_list.txt", package = "GRADA")

Analyze the Sequences:

This will render the DataTable (DT)

grada_analyze(PE = TRUE, seq = seq, read1 = read1, read2 = read2, M_min = 0)

find the first position of the adapter sequence

This will find the 1. position of the sequence (for mismatch = 0) in every read (that contains the adapter)

• the data from grada_analyze() is needed!

grada_analyze_positions(PE = TRUE, readlength = 125, numCores = 1)

Table of results:

This will show the found adapters in a table.

• data from grada_analyze() is needed.

DataTable (DT)

• for DT the package "DT" is needed.

grada_table_DT()

kable

grada_table_simple()

Plot the results:

This function will plot the found countings (for mismatch = 0)

• data from grada_analyze() is needed.
• data from grada_analyze_positions() is needed!

For the standard stettings all the three following commands are the same:

• grada_plot_bar(PE = TRUE, input = "temp/", skip = TRUE, plot_row = 2, plot_col = 2)
• grada_plot_bar()
• grada_plot()

grada_plot_bar(PE = TRUE, skip = TRUE, plot_row = 1, plot_col = 1)

LucasFVoges/GRADA documentation built on Feb. 16, 2021, 11:38 a.m.