clumpsAnalysis: Mutation enrichment analysis

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

Description

Conduct the mutation mapping analysis based on protein 3D structures

Usage

clumpsAnalysis(
  gene0,
  SNPlist0,
  gene_annotation0,
  pdb,
  sstart0,
  send0,
  input_dir = TRUE
)

Arguments

gene0	A gene systematic name
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 it is a residue distance matrix
sstart0	The start residue coordinate for the resdiues in the PDB file
send0	The end residue coordinate for the residues in the PDB file
input_dir	A logical vector

Value

p_value

Examples

# Load the gene feature gene and SNP dataset
data('gene_feature0')
data('snp_data')
# Annotate the SNP
mutated_gene <- annotateSNP(snp_input = snp_data, gene_feature = gene_feature0)
# Load the residue distance matrix
data('ResidueDistance_YPR184W')
# Get the SNP list for specific gene
mutated_gene1 <- filter(mutated_gene, Gene2 == 'YPR184W')
result0 <- clumpsAnalysis(gene0 = 'YPR184W',
                         SNPlist0 = mutated_gene1,
                         gene_annotation0 = gene_feature0,
                         pdb = ResidueDistance_YPR184W,
                         sstart0 = 2,
                         send0 = 1534,
                         input_dir= FALSE)

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