inst/doc/Vignette.R

In DominoEffect: Identification and Annotation of Protein Hotspot Residues

## ----setup, include = FALSE---------------------------------------------------
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("DominoEffect"))) 

## ---- eval=FALSE--------------------------------------------------------------
#  if (!require("BiocManager"))
#      install.packages("BiocManager")
#  BiocManager::install("DominoEffect")

## -----------------------------------------------------------------------------
library(DominoEffect)

## -----------------------------------------------------------------------------
data("TestData", package = "DominoEffect")
data("SnpData", package = "DominoEffect")
data("DominoData", package = "DominoEffect")

## ---- eval=FALSE--------------------------------------------------------------
#  DominoEffect(TestData, DominoData, SnpData)

## ---- eval=FALSE--------------------------------------------------------------
#  mutation_dataset = read.table ("user_file_with_mutations.txt", header = T)
#  gene_data = read.table ("user_ensembl_gene_list.txt", header = T)
#  snp_data = read.table ("user_population_SNPs_with_frequency.txt", header = T)

## ---- message = FALSE, results = "hide"---------------------------------------
hotspot_mutations <- DominoEffect(mutation_dataset = TestData, 
                                  gene_data = DominoData, snp_data = SnpData)

## ---- eval= FALSE-------------------------------------------------------------
#  data("TestData", package = "DominoEffect")

## ---- echo = FALSE------------------------------------------------------------
kable(head(TestData), row.names = FALSE)

## ---- echo = FALSE------------------------------------------------------------
kable(head(hotspot_mutations), row.names = FALSE)

## ---- eval = FALSE------------------------------------------------------------
#  hotspot_mutations <- DominoEffect(mutation_dataset, gene_data, snp_data, min_n_muts, MAF_thresh, flanking_region, poisson.thr, percentage.thr, ratio.thr, approach, write_to_file)

## -----------------------------------------------------------------------------
min_n_muts <- 5

## -----------------------------------------------------------------------------
MAF.thr <- 0.01

## -----------------------------------------------------------------------------
flanking_region <- c(200, 300)
flanking_region <- c(300)

## -----------------------------------------------------------------------------
poisson.thr <- 0.01

## -----------------------------------------------------------------------------
percentage.thr <- 0.15

## -----------------------------------------------------------------------------
ratio.thr <- 40

## -----------------------------------------------------------------------------
approach = "percentage"

## ---- eval = FALSE------------------------------------------------------------
#  write_to_file = "YES"

## ---- message = FALSE, results = "hide", eval = FALSE-------------------------
#  hotspot_mutations <- DominoEffect(mutation_dataset = TestData,
#                                    gene_data = DominoData, snp_data = SnpData)

## ---- message = FALSE---------------------------------------------------------
hotspot_mutations <- identify_hotspots(mutation_dataset = TestData, 
                                       gene_data = DominoData, 
                                       snp_data = SnpData, min_n_muts = 5, 
                                       MAF_thresh = 0.01, 
                                       flanking_region = c(200, 300), 
                                       poisson.thr = 0.01, 
                                       percentage.thr = 0.15, ratio.thr = 45, 
                                       approach = "percentage")

## ---- message = FALSE, eval = FALSE-------------------------------------------
#  results_w_annotations <- map_to_func_elem(hotspot_mutations,
#                                            write_to_file = "NO",
#                                            ens_release = "73")

## ---- echo = FALSE------------------------------------------------------------
kable(head(DominoData), row.names = FALSE)

## ---- echo = FALSE------------------------------------------------------------
kable(head(SnpData), row.names = FALSE)

## ---- echo = FALSE------------------------------------------------------------
hotspot_mutations.GPo <- GPo_of_hotspots(hotspot_mutations)
head(hotspot_mutations.GPo)

## -----------------------------------------------------------------------------
sessionInfo()