Nothing
# ``````````````````` #
# Load testing data #
# ................... #
# Load mass spectrometry data
load("../data/data-filterMS.RData")
# Construct filterMS objects
out_filterMS <- filterMS(msDatObj, paste0("frac", 3:4), "all", 0.05, 1000, 7L)
out_filterMS_bord_none <- filterMS(msDatObj, paste0("frac", 3:4), "none", 0.05, 1000, 7L)
out_filterMS_bord_1val <- filterMS(msDatObj, paste0("frac", 3:4), 0, 0.05, 1000, 7L)
out_filterMS_bord_2val <- filterMS(msDatObj, paste0("frac", 3:4), c(1, 99), 0.05, 1000, 7L)
out_filterMS_nfinal_none <- filterMS(msDatObj, paste0("frac", 3:4), c(1, 99), 0.05, 1e9, 7L)
# Obtain summary output in string form
out_v1 <- format(out_filterMS)
out_bord_none <- format(out_filterMS_bord_none)
out_bord_1val <- format(out_filterMS_bord_1val)
out_bord_2val <- format(out_filterMS_bord_2val)
out_nfinal_none <- format(out_filterMS_nfinal_none)
# ````````````````````````````````````` #
# Construct target results for out_v1 #
# ..................................... #
target_v1 <- list()
target_v1$newl <- "\n"
target_v1$regn <- paste0(
"The region of interest was specified as (2 fractions):\n",
"------------------------------------------------------\n",
" frac3\n",
" frac4\n",
"\n")
target_v1$bord <- paste0(
"The bordering regions were specified as \"all\"\n",
"---------------------------------------------\n",
" frac1\n",
" frac2\n",
" frac5\n",
" frac6\n",
"\n")
target_v1$fcri <- paste0(
"The filtering criteria was specified as:\n",
"----------------------------------------\n",
" minimum intensity: 1,000 \n",
" maximum charge: 7 \n",
" bordering region ratio: 0.05\n",
"\n")
target_v1$prir <- paste0(
"The mass spectrometry data prior to filtering had:\n",
"--------------------------------------------------\n",
" 24 compounds\n",
" 6 fractions\n",
"\n")
target_v1$frem <- paste0(
"Individually, each criterion reduced the 24 m/z levels to the following number:\n",
"-------------------------------------------------------------------------------\n",
" criterion 1: 20 (fraction with max. abundance is in region of interest)\n",
" criterion 2: 13 (fractions in bordering region have < 5 of max. abundance)\n",
" criterion 3: 18 (nonzero abundance in right adjacent fraction to max.)\n",
" criterion 4: 20 (at least 1 intensity > 1,000 in region of interest)\n",
" criterion 5: 20 (must have charge <= 7)\n",
"\n")
target_v1$ffin <- paste0(
"The total number of candidate compounds was reduced to:\n",
"-------------------------------------------------------\n",
" 4\n",
"\n")
target_v1 <- unlist(target_v1)
# `````````````````````````````````````````` #
# Construct targets for some special cases #
# .......................................... #
target_bord_none <- c(bord = paste0(
"The bordering regions were specified as \"none\"\n",
"----------------------------------------------\n",
" * no fraction names to show *\n",
"\n"))
target_bord_1val <- c(bord = paste0(
"The bordering regions were specified as each having length 0:\n",
"-------------------------------------------------------------\n",
" * no fraction names to show *\n",
"\n"))
target_bord_2val <- c(bord = paste0(
"The bordering regions were specified as having lengths 1 and 99:\n",
"----------------------------------------------------------------\n",
" frac2\n",
" frac5\n",
" frac6\n",
"\n"))
target_nfinal_none <- c(ffin = paste0(
"The total number of candidate compounds was reduced to:\n",
"-------------------------------------------------------\n",
" 0\n",
"\n"))
# ``````````````````````` #
# Save data for testing #
# ....................... #
save(out_v1, out_bord_none, out_bord_1val, out_bord_2val, out_nfinal_none,
target_v1, target_bord_none, target_bord_1val, target_bord_2val, target_nfinal_none,
file="tests/data/data-summary-filterMS.RData")
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