# ``````````````````` #
# Load testing data #
# ................... #
# Construct ms and bioactivity data
load("../data/data-rankEN-test.RData")
# Construct rankEN objects
out_rankEN_v1 <- rankEN(filterMS_obj, bioact, reg_idx, reg_idx, lambda)
out_rankEN_v2 <- rankEN(filterMS_obj, bioact, reg_idx, reg_idx, lambda, TRUE, 6)
out_rankEN_v2$summ_info$region_nm$ms[1:5 * 2L] <- c("asdf", "987321.555444333", "*", "<.>", "42")
out_rankEN_v2$summ_info$cmp_rm <- NULL
# Obtain summary output in string form
out_v1 <- format(out_rankEN_v1, 5L)
out_v2 <- format(out_rankEN_v2, 999)
# ````````````````````````````````````` #
# Construct target results for out_v1 #
# ..................................... #
target_v1 <- list()
target_v1$newl <- "\n"
target_v1$ddim <- paste0(
"Data dimensions (some compounds were removed):\n",
"----------------------------------------------\n",
" region of interest: 10\n",
" candidate compounds: 204\n",
" bioactivity replicates: 4\n",
"\n")
target_v1$crem <- paste0(
"Compounds removed for being constant:\n",
"-------------------------------------\n",
" Mass-to-charge Charge\n",
" -------------- ------\n",
" 501 701 \n",
" 502 702 \n",
" 503 703 \n",
" 504 704 \n",
"\n")
target_v1$regi <- paste0(
"Fractions included in region of interest:\n",
"-----------------------------------------\n",
" Mass spec. Bioactivity\n",
" ---------- -----------\n",
" ms21 bio21 \n",
" ms22 bio22 \n",
" ms23 bio23 \n",
" ms24 bio24 \n",
" ms25 bio25 \n",
" ms26 bio26 \n",
" ms27 bio27 \n",
" ms28 bio28 \n",
" ms29 bio29 \n",
" ms30 bio30 \n",
"\n")
target_v1$args <- paste0(
"Parameter arguments provided to rankEN:\n",
"---------------------------------------\n",
" Quadratic penalty parameter: 0.1\n",
" Consider only positive correlations: yes\n",
" Max number of candidate compounds: all\n",
"\n")
target_v1$rank <- paste0(
"Compounds in order of entrance (first 5 compounds, earliest at top):\n",
"--------------------------------------------------------------------\n",
" Mass spec. Charge Correlation\n",
" ---------- ------ -----------\n",
" 16 1 0.7847 \n",
" 2 1 0.7395 \n",
" 1 1 0.7474 \n",
" 186 1 0.6479 \n",
" 80 1 0.6866 \n",
"\n")
target_v1 <- unlist(target_v1)
# `````````````````````````````` #
# Construct targets for out_v2 #
# .............................. #
target_v2 <- list()
target_v2$newl <- "\n"
target_v2$ddim <- paste0(
"Data dimensions:\n",
"----------------\n",
" region of interest: 10\n",
" candidate compounds: 200\n",
" bioactivity replicates: 4\n",
"\n")
target_v2$rem <- ""
target_v2$regi <- paste0(
"Fractions included in region of interest:\n",
"-----------------------------------------\n",
" Mass spec. Bioactivity\n",
" ---------- -----------\n",
" ms21 bio21 \n",
" asdf bio22 \n",
" ms23 bio23 \n",
" 987321.555444333 bio24 \n",
" ms25 bio25 \n",
" * bio26 \n",
" ms27 bio27 \n",
" <.> bio28 \n",
" ms29 bio29 \n",
" 42 bio30 \n",
"\n")
target_v2$args <- paste0(
"Parameter arguments provided to rankEN:\n",
"---------------------------------------\n",
" Quadratic penalty parameter: 0.1\n",
" Consider only positive correlations: yes\n",
" Max number of candidate compounds: 6\n",
"\n")
target_v2$rank <- paste0(
"Compounds in order of entrance (all compounds, earliest at top):\n",
"----------------------------------------------------------------\n",
" Mass spec. Charge Correlation\n",
" ---------- ------ -----------\n",
" 16 1 0.7847 \n",
" 2 1 0.7395 \n",
" 1 1 0.7474 \n",
" 186 1 0.6479 \n",
" 80 1 0.6866 \n",
" 41 1 0.5002 \n",
"\n")
target_v2 <- unlist(target_v2)
# ``````````````````````` #
# Save data for testing #
# ....................... #
save(out_v1, out_v2, target_v1, target_v2,
file="../data/data-summary-rankEN.RData")
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