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renamed reg_cols_extraction.R to colnames_clinical_meds.R

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Tanushree Tunstall 2020-11-18 16:11:35 +00:00
parent 66f49a0eed
commit 702ff4e327
4 changed files with 5 additions and 29 deletions
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0
reg_cols_extraction.R → colnames_clinical_meds.R
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2
data_extraction_formatting_clinical.R
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@ -10,7 +10,7 @@ getwd()
# Input: source data # Input: source data
#==================== #====================
source("read_data.R") source("read_data.R")
source("reg_cols_extraction.R") source("colnames_clinical_meds.R")
######################################################################## ########################################################################
# quick sanity checks # quick sanity checks
table(adult_df$ia_exac_copd==1 & adult_df$asthma == 1) # check this is 4 table(adult_df$ia_exac_copd==1 & adult_df$asthma == 1) # check this is 4

2
data_extraction_formatting_regression.R
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@ -10,7 +10,7 @@ getwd()
# Input: source data for clinical # Input: source data for clinical
#==================== #====================
source("data_extraction_formatting_clinical.R") source("data_extraction_formatting_clinical.R")
#source("reg_cols_extraction.R") #source("colnames_clinical_meds.R")
#======================================= #=======================================
# Data for mediator to include in regression # Data for mediator to include in regression
#======================================= #=======================================

30
flu_stats_unpaired_clinical.R
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@ -20,31 +20,7 @@ source("data_extraction_formatting_clinical.R")
outfile_name_clinical = paste0("flu_stats_clinical_unpaired.csv") outfile_name_clinical = paste0("flu_stats_clinical_unpaired.csv")
outfile_clinical_unpaired = paste0(outdir_stats, outfile_name_clinical) outfile_clinical_unpaired = paste0(outdir_stats, outfile_name_clinical)
outfile_clinical_unpaired outfile_clinical_unpaired
#===============================
# data assignment for stats
#================================
wf = npa_wf[npa_wf$flustat == 1,]
lf = npa_lf[npa_lf$flustat == 1,]
lf$timepoint = paste0("t", lf$timepoint)
lf = lf[!lf$mediator == "vitd",]
########################################################################
# clear variables
rm(sam_lf, sam_wf
, serum_lf, serum_wf)
rm(colnames_sam_df, expected_rows_sam_lf
, colnames_serum_df, expected_rows_serum_lf)
rm(pivot_cols)
# sanity checks
table(lf$timepoint)
#if (table(lf$flustat) == table(npa_lf$flustat)[[2]]){
# cat("Analysing Flu positive patients for:", my_sample_type)
#}else{
# cat("FAIL: problem with subsetting data for:", my_sample_type)
# quit()
#}
######################################################################## ########################################################################
# Unpaired stats for clinical data b/w groups: wilcoxon UNpaired analysis # Unpaired stats for clinical data b/w groups: wilcoxon UNpaired analysis
# No correction required # No correction required
@ -73,9 +49,9 @@ gathercols <- c("age", "los", "onset2final", "onsfindeath", "onset_2_initial", "
clinical_lf = gather_(clinical_df_numerical, keycol, valuecol, gathercols) clinical_lf = gather_(clinical_df_numerical, keycol, valuecol, gathercols)
#============== #====================
# unpaired: t1 # unpaired: clinical
#============== #====================
sum(is.na(clinical_lf$value)) sum(is.na(clinical_lf$value))
foo = clinical_lf[which(is.na(clinical_lf$value)),] foo = clinical_lf[which(is.na(clinical_lf$value)),]