Commit 87b69a5b authored by joerg.buescher's avatar joerg.buescher
Browse files

changing names of default ML models and value of prm$tshiftfine in initialize_prm.R

parent 64c727b2
# initialize list of global parameters
prm <- list()
prm <- list()
# Model type
......@@ -8,11 +8,11 @@ prm <- list()
prm$ml_type <- 'mlprod'
# Comand line args
# Command line args
prm$polarmets <- TRUE
prm$sosomets <- FALSE
prm$expertmode <- FALSE
prm$fancyformat <- TRUE
prm$expertmode <- FALSE # additional debugging outputs
prm$fancyformat <- FALSE # add conditional formatting in excel output CAUTION: Incompatible with recent versions of MS excel. Works well with Libre Office.
prm$verbose <- 1
......@@ -20,9 +20,9 @@ prm$verbose <- 1
if (as.character(Sys.info()[["user"]]) == 'rstudio'){
prm$runninglocal <- TRUE
prm$pathprefix <- '/home/rstudio/'
} else {
# Set testing environemt
} else {
# Set testing environment
prm$runninglocal <- FALSE
prm$pathprefix <- '/'
}
......@@ -32,7 +32,7 @@ prm$log_con <- file("R_messages.log",open="a")
# Set global parameters for peak detection
prm$timerange <- c(0,5) # time range in minutes --> will be re-determined based on first sample further down
prm$samplingfrequency <- 2 # samplingfrequency (time resolution of analysis) in Hz
prm$samplingfrequency <- 2 # samplingfrequency (time resolution of analysis) in Hz
prm$corwindow <- 5 # number of data points for calculation of correlation among traces
prm$smoothnum <- 9 # k for rollmean smoothing of traces
prm$corcutoff <- 0.9 # minimum correlation among traces to seach for a peak
......@@ -47,45 +47,28 @@ prm$quartile_range_factor <- 3 #factor to spread interquartile range for peak
prm$initial_candidates <- 5 # to be used in qqq_mrm_integrage
prm$timewindow <- 1.5 # time window for correlating
prm$tshiftcrude <- seq(-60,60,2) # steps for time shift test
prm$tshiftfine <- seq(-15,15,1) # steps for time shift fine adjustment
prm$tshiftfine <- seq(-30,30,1) # steps for time shift fine adjustment
prm$microsearch <- seq(-6,6,1) # steps for microsearch of minimum when propagating consensus peak to single chromatograms
prm$nmet <- 0 # number of metabolites, will be updated later
prm$nsmpl <- 0 # number of samples, will be updated later
prm$polarities = list('Positive'= '+','Negative'= '-','-'='Negative','+'='Positive')
# Paths and columns
# prm$RTcolumn <- 'LunaNH2.RT.QQQ'
# prm$excelfile <- paste0(prm$pathprefix, 'data/helperfiles/metabolite_databases/AgilentQQQdb.xlsx') # polar is default
prm$model_rf_path <- paste0(prm$pathprefix, 'data/helperfiles/testdata/LC_machine_learning/rf_model_pcand.Rdata')
prm$model_rf_final_path <- paste0(prm$pathprefix, 'data/helperfiles/testdata/LC_machine_learning/rf_model_finalp.Rdata')
prm$model_rf_path <- paste0(prm$pathprefix, 'data/helperfiles/testdata/LC_machine_learning/model_pcand.Rdata')
prm$model_rf_final_path <- paste0(prm$pathprefix, 'data/helperfiles/testdata/LC_machine_learning/model_finalp.Rdata')
#Rouse?
prm$train_path <- "" #must be set until intermdiate pipeline is replaced
prm$train_path <- "" #must be set until intermediate pipeline is replaced
#?
prm$sum12c <- FALSE #?any(prm$args == '--sum12c') # sum 12c qual and quant area/height #?
# option to use sum of quantifier and 12C qualifier as intensity value instead of only quantifier
prm$sum12c <- FALSE # sum 12c qual and quant area/height
# Polarmets
prm$polarmets <- TRUE
prm$sosomets <- FALSE
prm$excelfile <- paste0(prm$pathprefix, 'data/helperfiles/metabolite_databases/metabdb_really_polar.xlsx')
prm$RTcolumn <- 'RT'
# # get date of measurement
# prm$measureddate <- tryCatch({
# prm$sampleinfo <- read.csv('sample.info', stringsAsFactors = FALSE)
# prm$measureddate <- prm$sampleinfo[1,'measureddate']
# prm$test <- as.Date(prm$measureddate) # check if date can be parsed
# } , error = function(err) {
# prm$test <- as.Date("2017-11-08 00:00:00")
# })
# if (prm$measureddate < as.Date('2019-05-01')) { # switch to AmCarb buffer
# prm$RTcolumn <- 'LunaNH2.RT.QQQ' #changed
# } else {
# prm$RTcolumn <- 'LunaNH2.RT.QQQ.AmCarb' #changed
# }
# Lipids
# prm$polarmets <- FALSE
......
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