readGenome: Read genome data from user

In quick2063706271/Cov2Comparator: Analyzing SARS covid-2 genome across different geographic regions

Description

A function that read genome sequence .fasta file from user by inputting directories

Usage

readGenome(fastaFile, nameToRegionsFile = NULL)

Arguments

fastaFile	A string indicating the path of .fasta file
nameToRegionsFile	A string indicating the path of name to region .csv file

Value

Returns a DNAStringSet with sequences from fastaFile are add.

References

H. Pagès, P. Aboyoun, R. Gentleman and S. DebRoy (2020). Biostrings: Efficient manipulation of biological strings. R package version 2.58.0. https://bioconductor.org/packages/Biostrings

Examples

# Example 1
# Load MN985325.1.fasta and MT066156.1.fasta file in inst/extdata
fastaPath1 <- system.file("extdata", "MN985325.1.fasta",
  package="Cov2Comparator")
fastaPath2 <- system.file("extdata", "MT066156.1.fasta",
  package="Cov2Comparator")
nameToRegionsFile <- system.file("extdata", "nameToCountry.txt",
  package="Cov2Comparator")
fasta1 <- readGenome(fastaPath1, nameToRegionsFile)

quick2063706271/Cov2Comparator documentation built on Dec. 22, 2021, 10:59 a.m.