vcf2df: Return a dataframe object with gene mutation information

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

Description

Perform vcf file retrieving using read.vcfR function, result stored in standarlize data.frame for easy usage.

Usage

vcf2df(filepath)

Arguments

filepath

The path directed to vcf file on current working directory

Value

Return a data.frame object contain vcf document loaded

• CHROM - Located in chromosome CHROM

• POS - The start position of the mutation

• ID - ID of the mutation (if available)

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

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

• CONSEQUENCE - Record the effect of mutation under biological studies

• OCCURRENCE - Record the associated cancer and its distribution

• affected_donors - Record the total number of donor affected

• project_count - Number of project associated with current studies

Author(s)

Sijie Xu, [e-mail]

References

Knaus BJ, Grünwald NJ (2017). “VCFR: a package to manipulate and visualize variant call format data in R." _Molecular Ecology Resources_, *17*(1), 44-53. ISSN 757, <URL: http://dx.doi.org/10.1111/1755-0998.12549>.

Examples

filePath <- system.file("extdata", "test.vcf", package = "rseAnalysis")
vcf <- vcf2df(filePath)

JackXu2333/rseAnalysis documentation built on Dec. 31, 2020, 1:10 p.m.