hotSpotAnalysis: Mutation hotspot analysis

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

Description

Conduct the mutation hotspot analysis based on protein 3D structures

Usage

hotSpotAnalysis(
  gene0 = ss0,
  pdbID = NA,
  SNPlist0 = mutated_gene1,
  gene_annotation0 = gene_feature0,
  pdb = distance,
  sstart0 = p1,
  send0 = p2,
  qstart0 = q1,
  qend0 = q2,
  result_dir = outfile0,
  strain_type = NA,
  input_dir = TRUE
)

Arguments

gene0	A gene systematic name
pdbID	A string
SNPlist0	A SNP list for the strains from specific phenotype
gene_annotation0	The gene annotation summary
pdb	The dir store the residue distance matrix, should be a txt file seperated by ',' or the residue distance matrix
sstart0	The start residue coordinate for the resdiues in the original protein
send0	The end residue coordinate for the residues in the the original protein
qstart0	The start residue coordinate for the resdiues in the PDB file
qend0	The end residue coordinate for the residues in the PDB file
result_dir	The directory to save the hot spot analysis result
strain_type	A string to represent the source of SNP
input_dir	A logical vector

Value

A dataframe contains the hotspot analysis result

Examples

# Load SNP data and residue distance matrix
data("snp_YBR046C")
data("ResidueDistance_YBR046C")
# Creat file to store the result
outfile0 <- "result/hot_spot_analysis"
dir.create(outfile0)
hotSpotAnalysis(
gene0 = "YBR046C",
 SNPlist0 = snp_YBR046C,
 gene_annotation0 = gene_feature0,
 pdb = ResidueDistance_YBR046C,
 sstart0 = 5, # coordinate of original protein residues sequence
 send0 = 333, # coordinate of original protein residues sequence
 qstart0 = 1, # coordinate of protein residues sequence in pdb file
 qend0 = 329, # coordinate of protein residues sequence in pdb file
 result_dir = outfile0,
 input_dir = FALSE
)

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