# ```````````````````````` #
# Construct testing data #
# ........................ #
# Load mass spectrometry data
load("../data/data-binMS.RData")
out_binMS_v1 <- binMS(testMS, "mtoz", "chg", "mass", "time", c("ms1", "ms2"),
c(14, 45), c(2e3, 15e3), c(2, 10), 0.05, 1)
out_v1 <- format(out_binMS_v1)
# ````````````````````````````````````` #
# Construct target results for out_v1 #
# ..................................... #
target_v1 <- list()
target_v1$newl <- "\n"
target_v1$incl <- paste0(
"The inclusion criteria was specified as follows:\n",
"------------------------------------------------\n",
" time of peak retention: between 14 and 45\n",
" mass: between 2,000 and 15,000\n",
" charge: between 2 and 10\n",
"\n")
target_v1$cons <- paste0(
"m/z levels were consolidated when each of the following criteria were met:\n",
"--------------------------------------------------------------------------\n",
" m/z levels were no more than 0.05 units apart\n",
" the time peak retention occured no farther apart than 1 units\n",
" the charge states were the same\n",
"\n")
target_v1$size <- paste0(
"The mass spectrometry data prior to binning had:\n",
"------------------------------------------------\n",
" 75 m/z levels\n",
"\n")
target_v1$nrem <- paste0(
"The number of remaining m/z levels after filtering by the inclusion criteria was:\n",
"---------------------------------------------------------------------------------\n",
" time of peak retention: 69\n",
" mass: 68\n",
" charge: 68\n",
" satisfied all: 56\n",
"\n")
target_v1$ntot <- paste0(
"After consolidating the m/z levels, there were:\n",
"-----------------------------------------------\n",
" 22 levels\n",
"\n")
target_v1 <- unlist(target_v1)
# `````````````````````````````````````````` #
# Construct out_v2 (a variation on out_v1) #
# .......................................... #
# Temporarily construct as a list for convenience, will 'unlist' later
out_binMS_v2 <- out_binMS_v1
# Inclusion criteria
out_binMS_v2$summ_info$time_range[1L] <- 12.99
out_binMS_v2$summ_info$mass_range[2L] <- 101.1
out_binMS_v2$summ_info$charge_range[1L] <- -2.3
# Consolidation criteria
out_binMS_v2$summ_info$time_diff <- 1234.56
# Size prior to binning
out_binMS_v2$summ_info$n_tot <- 1055
# Individual filtering remaining
out_binMS_v2$summ_info$n_time_pr <- 1001
# Total remaining
out_binMS_v2$summ_info$n_binned <- 5678
out_v2 <- format(out_binMS_v2)
# ````````````````````````````````````` #
# Construct target results for out_v2 #
# ..................................... #
# Temporarily construct as a list for convenience, will 'unlist' later
target_v2 <- list()
target_v2$newl <- "\n"
target_v2$incl <- paste0(
"The inclusion criteria was specified as follows:\n",
"------------------------------------------------\n",
" time of peak retention: between 12.99 and 45 \n",
" mass: between 2,000 and 101.1\n",
" charge: between -2.3 and 10 \n",
"\n")
target_v2$cons <- paste0(
"m/z levels were consolidated when each of the following criteria were met:\n",
"--------------------------------------------------------------------------\n",
" m/z levels were no more than 0.05 units apart\n",
" the time peak retention occured no farther apart than 1,234.56 units\n",
" the charge states were the same\n",
"\n")
target_v2$size <- paste0(
"The mass spectrometry data prior to binning had:\n",
"------------------------------------------------\n",
" 1,055 m/z levels\n",
"\n")
target_v2$nrem <- paste0(
"The number of remaining m/z levels after filtering by the inclusion criteria was:\n",
"---------------------------------------------------------------------------------\n",
" time of peak retention: 1,001\n",
" mass: 68\n",
" charge: 68\n",
" satisfied all: 56\n",
"\n")
target_v2$ntot <- paste0(
"After consolidating the m/z levels, there were:\n",
"-----------------------------------------------\n",
" 5,678 levels\n",
"\n")
target_v2 <- unlist(target_v2)
# ``````````````````````` #
# Save data for testing #
# ....................... #
save(out_v1, out_v2, target_v1, target_v2,
file="tests/data/data-summary-binMS.RData")
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