RNA.validate: Apply DNA mutation to RNA and validate the file

In JackXu2333/dseAnalysis: Correlation analysis of RNA secondary structure mutation and differential expression

Description

Calculate the mutated series of RNA from RNA fasta, bed file , and DNA vcf file, both should be result file from vcf2df and fasta2df file, function gives validation based on fasta and vcf comparisons, user should user validation result to make sure their vcf and fasta file are aligned under same version. Algorithm inspired by the mRNA mutation function, a utility function created by Sijie Xu and Zhiwen Tan, the updated method here is a more generalized and input validated method, more checking are embeded to insure the mutation is applied correctly.

Usage

RNA.validate(fasta, vcf, bed)

Arguments

fasta	RNA sequence to be matched read using fasta2df
vcf	mutation information read using vcf2df function
bed	bed information read using bed2df function

Value

Return the RNA.mutated data frame that includes all information about the RNA and its information

• NAME - Corresponding of the RNA sequence

• MATCH - Boolean value indicating whether the mutation can be applied, FALSE value indicate the sequence given has inconsistent bases comparing to the reference base in VCF file

• STAPOS - The start location of the sequence

• ENDPOS - The end location of the sequence

• DIR - The direction of the sequence

• SEQ - The original RNA sequence

• CUR.REF - The current RNA base(s) on the mutation point

• MUT.REF - The reference base(s) on the mutation point

• MUT.ALT - The alternative base(s) appeared in during mutation

• MUT.SEQ - The mutated RNA sequence when MATCH is TRUE, otherwise empty string

• MUT.POS - The start position of the mutation

Author(s)

Sijie Xu, [e-mail]

References

Xu, S. Tan, Z., BCB430 "Analysis.zip/File Validation.rmd" <https://github.com/Deemolotus/BCB330Y-and-BCB430Y> Steipe B., ABC R Project, A Bioinformatics Course: Applied Bioinformatics http://steipe.biochemistry.utoronto.ca/abc/index.php/Bioinformatics_Main_Page

Examples

mutated <- RNA.validate(
              fasta = fasta2df(system.file("extdata", "test.fasta", package = "rseAnalysis")),
              vcf = vcf2df(system.file("extdata", "test.vcf", package = "rseAnalysis")),
              bed = bed2df(system.file("extdata", "test.bed", package = "rseAnalysis")))

JackXu2333/dseAnalysis documentation built on Dec. 31, 2020, 1:09 p.m.