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import.R
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import.R
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# Import and wrangling of the manuscript data
#
# The local STIGMA cohort dataset encompasses readouts of inflammation
# and metabolic markers of neurotransmitter precursors along with the
# explanatory variables (anxiety/depression signs and persistent symptoms)
# and confounders (age and sex)
#
# The INCOV validation dataset contains selected metabolites of the TRP decay
# pathway (so called TRYCATS pathway) and key inflammatory cytokines measured
# in blood of healthy individuals and COVID-19 participants at consecutive time
# points (acute, sub-acute and recovery) after clnical onset.
# tools --------
library(plyr)
library(tidyverse)
library(soucer)
library(trafo)
library(stringi)
library(readxl)
library(foreign)
insert_head()
c('./tools/globals.R',
'./tools/tools.R') %>%
source_all(message = TRUE, crash = TRUE)
# Sourcing the import scripts for single studies ------
insert_msg('Sourcing the import scripts')
source_all(c('./import scripts/local.R',
'./import scripts/incov.R'),
message = TRUE, crash = TRUE)
# Updating the project globals ------
insert_msg('Project globals')
globals$incov_lexicon <-
rbind(incov$annotation_proteome %>%
filter(variable %in% globals$incov_proteins),
incov$annotation_metabolome %>%
filter(variable %in% globals$incov_metabolites))
# END -----
insert_tail()