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perfomed LR analysis and tidyed up clinical formatting code

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This commit is contained in:
Tanushree Tunstall 2020-11-24 18:46:47 +00:00
parent 08e01abfb5
commit f0c0fd72d1
5 changed files with 296 additions and 301 deletions
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38
read_data.R
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@ -66,10 +66,6 @@ if (table(fp_adults$flustat == 1)[[1]] == nrow(fp_adults) ){
} else{
cat ("\nFAIL: adult df number mismatch!")
}
#=============================================
# FLU positive adult patients: without asthma
#=============================================
#-----------------------------------
# asthma and copd status correction
# for conflicting field!
@ -101,18 +97,21 @@ if ( table(fp_adults$ia_exac_copd, fp_adults$asthma) [[2,2]] == 0 ){
quit()
}
cat("\nExtracting flu positive without asthma")
table(fp_adults$asthma)
cat("\nNo. of asthmatics:", table(fp_adults$asthma)[[2]]
, "\nNo. of non-asthmatics:", table(fp_adults$asthma)[[1]])
str(fp_adults$asthma)
#=============================================
# FLU positive adult patients: without asthma
#=============================================
#cat("\nExtracting flu positive without asthma")
#table(fp_adults$asthma)
#cat("\nNo. of asthmatics:", table(fp_adults$asthma)[[2]]
# , "\nNo. of non-asthmatics:", table(fp_adults$asthma)[[1]])
#str(fp_adults$asthma)
table(fp_adults$obesity)
table(fp_adults$obesity, fp_adults$asthma)
#table(fp_adults$obesity)
#table(fp_adults$obesity, fp_adults$asthma)
fp_adults_na = fp_adults[fp_adults$asthma == 0,]
table(fp_adults_na$obesity)
table(fp_adults_na$obesity, fp_adults_na$asthma)
#fp_adults_na = fp_adults[fp_adults$asthma == 0,]
#table(fp_adults_na$obesity)
#table(fp_adults_na$obesity, fp_adults_na$asthma)
#============
# hc
@ -120,4 +119,13 @@ table(fp_adults_na$obesity, fp_adults_na$asthma)
#hc_data<- read.csv("/home/backup/MOSAIC/MEDIATOR_Data/master_file/Mediators_for_HC.csv")
#str(hc_data)
#table(hc_data$Timepoint, hc_data$Sample)
########################################################################
########################################################################
# quick sanity checks
table(adult_df$ia_exac_copd==1 & adult_df$asthma == 1) # check this is 4
table(fp_adults$ia_exac_copd==1 & fp_adults$asthma == 1) # check this is 3
# clear unnecessary variables
rm(metadata_all)
rm(all_df, adult_df)