#!/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_data = 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") clinical_cols_added = c("age_bins" , "o2_sat_bin" , "onset_initial_bin" , "steroid_ics" , "t1_resp_recoded" ) clinical_cols = c(clinical_cols_data, clinical_cols_added) 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() }