preprocessSNP: Prepare SNPs list for one gene

In hongzhonglu/Yeastspot3D: Mutation mapping analysis with protein 3D structure for yeast

Description

Proprocess all the snp for one gene belong to a sample set it should be noted that if the gene belong to minus strand, changeATCG function will be used be careful about the file directory

Proprocess all the snp for one gene belong to a sample set it should be noted that if the gene belong to minus strand, changeATCG function will be used be careful about the file directory

Usage

preprocessSNP(gene0, gene_feature, snp_files_dir0 = "data/gene_snp/")

preprocessSNP(gene0, gene_feature, snp_files_dir0 = "data/gene_snp/")

Arguments

gene0	A string representing the gene systematic name
gene_feature	A dataframe contains the detailed annotation of gene from database
snp_files_dir0	A fold dir contains the detailed snp information for each gene

Value

A dataframe contains each SNP information which including: chrosome, geneName, ref, alf and completment sign

A dataframe contains each SNP information which including: chrosome, geneName, ref, alf and completment sign

Examples

data('gene_feature0')
preprocessSNP(gene0 = 'YPR184W', gene_feature = gene_feature0, snp_files_dir0 = "data/gene_snp/")
data('gene_feature0')
preprocessSNP(gene0 = 'YPR184W', gene_feature = gene_feature0)

hongzhonglu/Yeastspot3D documentation built on March 28, 2020, 6:06 p.m.