seqCompareAsFile: Calculate the difference between gene sequences

In Deemolotus/gscVisualizer: Visualize The Difference among Gene Sequences

Description

A function that calculates the difference between gene sequences, takes an .fa file as function arguments, the default reference is the first sequence in the .fa file the function returns a list shows all differences. For coding genes, the difference are calculated based on the amino acid sequence. For noncoding gene, the difference are calculated based on Needleman–Wunsch algorithm.

Usage

seqCompareAsFile(seqType, type, filePath)

Arguments

seqType	The sequence ID for refernce sequence.
type	A string indicating either the comparison is for coding gene, or noncoding gene. type = "coding" or type = "noncoding".
filePath	A string shows the path for the specific .fa file

Value

Returns an List object of class seqCompareAsInput with results.

• id - A string name for the correspond sequence.

• sequences - A string indicate the sequence.

• difference - A value of class "numeric" indicating the difference between this sequence and reference sequence.

References

Charif D, Lobry J (2007). “SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis.” In Bastolla U, Porto M, Roman H, Vendruscolo M (eds.), Structural approaches to sequence evolution: Molecules, networks, populations, series Biological and Medical Physics, Biomedical Engineering, 207-232. Springer Verlag, New York. ISBN : 978-3-540-35305-8.

Kevin R. Coombes (2020). NameNeedle: Using Needleman-Wunsch to Match Sample Names. R package version 1.2.6/r51. Link

Pagès H, Aboyoun P, Gentleman R, DebRoy S (2020). Biostrings: Efficient manipulation of biological strings. R package version 2.58.0, Link.

Examples

# Examples 1:
# Using a .fa file for miRNA, use this file to
# Calculate the difference
filePath <- system.file("extdata", "test.fa", package = "gscVisualizer")
seqCompareAsFile("RNA", "noncoding", filePath)

# Examples 2:
# Using a .fa file for DNA sequence, use this file to
# Calculate the difference
filePath <- system.file("extdata", "seqCompareAsFileTest.fa", package = "gscVisualizer")
seqCompareAsFile("DNA", "coding", filePath)

Deemolotus/gscVisualizer documentation built on Dec. 31, 2020, 11:55 a.m.