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

library(knitr)
# knitr::opts_knit$set(root.dir = normalizePath("/Users/mbuljan/Documents/Paket_op/DominoEffect_radna/inst/doc"))
#library(devtools)
#knitr::opts_knit$set(root.dir = normalizePath(inst("Yeastspot3D"))) 

The package can be directly installed from the GitHub.

library(devtools)
install_github("hongzhonglu/Yeastspot3D",dependencies =TRUE)

Running the package

Load the package before starting the analysis.

library(Yeastspot3D)
loadPackageForSNPanalysis()

Mutation enrichment analysis

data('gene_feature0', package = "Yeastspot3D")
data('snp_data', package = "Yeastspot3D")
data('ResidueDistance_YPR184W', package = "Yeastspot3D")
mutated_gene <- annotateSNP(snp_input = snp_data, gene_feature = gene_feature0)
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)

Mutation hotspot analysis

# run the function
data('snp_YBR046C')
data('ResidueDistance_YBR046C')
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.