Commit 688437c3 authored by daniel.eilertz's avatar daniel.eilertz
Browse files

Stuff

parent 33107f74
......@@ -22,7 +22,7 @@ initialize_prm <- function() {
prm$verbose <- 1
# Check if local or on server ------------------------------
# Check if local or on server
if (as.character(Sys.info()[["user"]]) == 'rstudio'){
prm$runninglocal <- TRUE
prm$pathprefix <- '/home/rstudio/'
......@@ -45,8 +45,8 @@ initialize_prm <- function() {
prm$groupmetsearchwindow <- 90 # search window in seconds
prm$minNormArea <- 10000 # minimum median area of 13C ISTD to use for normalization
prm$minwidth <- 4 # minimum peak width in seconds
prm$qscutoff <- c(0.8,0.6) #0.72 #minimum quality score to report a peak [1] used for outliers [2] used for peaks within RT range
prm$quartile_range_factor <- 3 #factor to spread interquartile range for peak's RT outlier detection
prm$qscutoff <- c(0.8,0.6) # 0.72 - minimum quality score to report a peak [1] used for outliers [2] used for peaks within RT range
prm$quartile_range_factor <- 3 # factor to spread interquartile range for peak's RT outlier detection
prm$initial_candidates <- 5 # to be used in qqq_mrm_integrage
prm$timewindow <- 1.5 # time window for correlating
prm$tshiftcrude <- seq(-60,60,2) # steps for time shift test
......@@ -66,7 +66,7 @@ initialize_prm <- function() {
#?
prm$sum12c <- FALSE # sum 12c qual and quant area/height #
# Polarmets
# Polarmets as default
prm$polarmets <- TRUE
prm$sosomets <- FALSE
prm$excelfile <- paste0(prm$pathprefix, 'data/helperfiles/metabolite_databases/metabdb_really_polar.xlsx')
......
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