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added data_extraction_formatting_regression.R flu_stats_unpaired_clinical.R and reg_cols_extraction.R

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Tanushree Tunstall 2020-11-18 16:01:29 +00:00
parent bb6e92fa0f
commit 76dc3fbb6b
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#!/usr/bin/Rscript
getwd()
setwd('~/git/mosaic_2020/')
getwd()
########################################################################
# TASK: Extract relevant columns from mosaic fp adults data for regression
# clinical and sig meds
########################################################################
########################################################################
clinical_cols = c("mosaic"
, "ia_exac_copd"
, "death"
#, "obese2" #inc peaeds, but once you subset data for adults, its the same!
, "obesity"
, "flustat"
, "sfluv"
, "h1n1v"
, "age"
, "gender"
, "asthma"
, "vl_pfu_ul_npa1"
, "los"
, "onset2final"
, "onsfindeath"
, "onset_2_initial"
, "o2_sat_admis"
, "o2_sat_suppl"
, "ethnicity"
, "smoking"
, "ia_cxr"
, "max_resp_score"
, "T1_resp_score"
, "com_noasthma"
, "T2_resp_score"
, "inresp_sev"
, "steroid")
sig_npa_cols = c("eotaxin_npa1"
, "eotaxin3_npa1"
, "eotaxin3_npa2"
, "gmcsf_npa2"
, "ifnb_npa1"
, "ifnb_npa2"
, "il1_npa1"
, "il1_npa2"
, "il10_npa1"
, "il12p70_npa1"
, "il12p70_npa2"
, "il13_npa1"
, "il2_npa3"
, "il4_npa1"
, "il5_npa1"
, "il5_npa2"
, "il6_npa1"
, "il6_npa2"
, "il8_npa1"
, "il8_npa2"
, "il8_2_npa1"
, "il8_2_npa2"
, "ip10_npa1"
, "mcp4_npa1"
, "mcp4_npa2"
, "mdc_npa1"
, "mip17_npa1"
, "mip17_npa2"
, "neopterin_npa1"
, "rantes_npa1"
, "tarc_npa2"
, "tnf_npa2"
, "tnfr1_npa1"
, "tnfr1_npa2"
, "tnfr1_npa3"
, "tnfr2_npa1"
, "tnfr2_npa2"
, "tnfr2_npa3")
cols_to_extract = c(clinical_cols, sig_npa_cols)
if ( length(cols_to_extract) == length(clinical_cols) + length(sig_npa_cols) ){
cat("PASS: length match"
, "\nTotal no. of cols to extract for regression:", length(cols_to_extract)
, "\nNo. of clinical cols:", length(clinical_cols)
, "\nNo. of sig npa cols: ", length(sig_npa_cols))
}else{
cat("FAIL: length mismatch"
, "\nAborting!")
quit()
}