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

Description Usage Arguments Value Author(s) References Examples

View source: R/Mutation.R

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

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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

Author(s)

Sijie Xu, sijie.xu@mail.utoronto.ca

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

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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/rseAnalysis documentation built on Dec. 31, 2020, 1:10 p.m.