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## ----setup, cache=FALSE, include=FALSE--------------------------------------------------
library(knitr)
knit_theme$set("default")
opts_chunk$set(cache=FALSE)
opts_knit$set(root.dir=normalizePath(".."))
options(width=90)
# Convenience function
fcom <- function(x) format(x, big.mark=",")
## ----reading-data-ms--------------------------------------------------------------------
library(PepSAVIms)
# Load mass spectrometry data into memory
data(mass_spec)
## ----reading-data-bioact----------------------------------------------------------------
# Load bioactivity data into memory
data(bioact)
## ----bin-info, echo=FALSE---------------------------------------------------------------
# Perform mass spectrometry levels consolidation
bnfo <- binMS(mass_spec = mass_spec,
mtoz = "m/z",
charge = "Charge",
mass = "Mass",
time_peak_reten = "Reten",
ms_inten = NULL,
time_range = c(14, 45),
mass_range = c(2000, 15000),
charge_range = c(2, 10),
mtoz_diff = 0.05,
time_diff = 60)$summ_info
## ----consolidating-data-----------------------------------------------------------------
# Perform mass spectrometry levels consolidation
bin_out <- binMS(mass_spec = mass_spec,
mtoz = "m/z",
charge = "Charge",
mass = "Mass",
time_peak_reten = "Reten",
ms_inten = NULL,
time_range = c(14, 45),
mass_range = c(2000, 15000),
charge_range = c(2, 10),
mtoz_diff = 0.05,
time_diff = 60)
# Show some summary information describing the consolidation process
summary(bin_out)
## ----filtering-data---------------------------------------------------------------------
# Perform mass spectrometry levels filtering
filter_out <- filterMS(msObj = bin_out,
region = paste0("VO_", 17:25),
border = "all",
bord_ratio = 0.01,
min_inten = 1000,
max_chg = 10)
# Show summary information describing the filtering process
summary(filter_out)
## ----candidate-compound-ranking---------------------------------------------------------
# Rank the candidate compounds using the ranking procedure for each of the
# bioactivity datasets
rank_oc <- rankEN(msObj = filter_out,
bioact = bioact$oc,
region_ms = paste0("VO_", 18:22),
region_bio = paste0("VO_", 18:22),
lambda = 0.001)
rank_bc <- rankEN(msObj = filter_out,
bioact = bioact$bc,
region_ms = paste0("VO_", 18:22),
region_bio = paste0("VO_", 18:22),
lambda = 0.001)
rank_pc <- rankEN(msObj = filter_out,
bioact = bioact$pc,
region_ms = paste0("VO_", 18:23),
region_bio = paste0("VO_", 18:23),
lambda = 0.001)
rank_ab <- rankEN(msObj = filter_out,
bioact = bioact$ab,
region_ms = paste0("VO_", 17:21),
region_bio = paste0("VO_", 17:21),
lambda = 0.001)
rank_pa <- rankEN(msObj = filter_out,
bioact = bioact$pa,
region_ms = paste0("VO_", 18:21),
region_bio = paste0("VO_", 18:21),
lambda = 0.001)
rank_ec <- rankEN(msObj = filter_out,
bioact = bioact$ec,
region_ms = paste0("VO_", 18:25),
region_bio = paste0("VO_", 18:25),
lambda = 0.001)
rank_fg <- rankEN(msObj = filter_out,
bioact = bioact$fg,
region_ms = paste0("VO_", 19:24),
region_bio = paste0("VO_", 19:24),
lambda = 0.001)
## ----cyO2-rankings----------------------------------------------------------------------
# Function to find the rank of cyO2 compounds
find_cyO2_rank <- function(rankEN_obj) {
# The m/z values for the two incarnations of cyO2
mval1 <- 1047.4897758000001886
mval2 <- 1570.2413587500000176
# Find the indices (corresponding to the ranks) of the cyO2 incarnations
which((rankEN_obj$mtoz == mval1 & rankEN_obj$charge == 3) |
(rankEN_obj$mtoz == mval2 & rankEN_obj$charge == 2))
}
# List the ranks for cyO2
lapply(list(ab=rank_ab, bc=rank_bc, ec=rank_ec, fg=rank_fg,
oc=rank_oc, pa=rank_pa, pc=rank_pc),
find_cyO2_rank)
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