printSNPforGene: Print the mutated residues

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

Description

Output all the mutated residues information

Usage

printSNPforGene(
  gene0 = ss0,
  SNPlist0 = mutated_gene1,
  gene_annotation0 = gene_feature0,
  pdbID0 = pdbID,
  sstart0 = p1,
  send0 = p2
)

Arguments

gene0	A gene systematic name
SNPlist0	A SNP list for the strains from specific phenotype
gene_annotation0	The gene annotation summary
pdbID0	A pdb id which has been mapped onto the gene name (the first parameter)
sstart0	The start residue coordinate for the resdiues in the PDB file
send0	The end residue coordinate for the residues in the PDB file

Value

A dataframe contains the mutated residues information

Examples

data('gene_feature0')
data('snp_data')
mutated_gene <- annotateSNP(snp_input = snp_data, gene_feature = gene_feature0)
data('ResidueDistance_YPR184W')
mutated_gene1 <- filter(mutated_gene, Gene2 == 'YPR184W')
pdbID <- '2_1534_5d06.1.A_5b2453487f4bf94bf75ead43'
SNP_list <- printSNPforGene(gene0 = 'YPR184W',
                            SNPlist0 = mutated_gene1,
                            gene_annotation0 = gene_feature0,
                            pdbID0 = pdbID,
                            sstart0 = 2,
                            send0 = 1534)

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