From 47a03c2639d9b7177c711b01f68df6f8bf2724c6 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Fri, 27 Nov 2020 18:21:35 +0000 Subject: [PATCH] saving work --- data_extraction_mediators.R | 48 ++++++++++++++++++------------------- 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/data_extraction_mediators.R b/data_extraction_mediators.R index f8c24b8..2d224fd 100755 --- a/data_extraction_mediators.R +++ b/data_extraction_mediators.R @@ -50,16 +50,16 @@ if( length(sam_cols_clean) == length(sam_cols) - length(sam_cols_to_omit) ){ , "Got:", length(sam_cols_clean) ) } -sam_cols_to_extract = c(meta_data_cols, sam_cols_clean) +sam_cols_to_extract = c(meta_clinical_cols, sam_cols_clean) cat("Extracting SAM cols + metadata_cols") -if ( length(sam_cols_to_extract) == length(meta_data_cols) + length(sam_cols_clean) ){ +if ( length(sam_cols_to_extract) == length(meta_clinical_cols) + length(sam_cols_clean) ){ cat("Extracing", length(sam_cols_to_extract), "columns for sam") sam_df = my_data[, sam_cols_to_extract] }else{ cat("FAIL: length mismatch" - , "Expeceted to extract:", length(meta_data_cols) + length(sam_cols_clean), "columns" + , "Expeceted to extract:", length(meta_clinical_cols) + length(sam_cols_clean), "columns" , "Got:", length(sam_cols_to_extract)) } @@ -90,16 +90,16 @@ if( length(serum_cols_clean) == length(serum_cols) - length(serum_cols_to_omit) , "Got:", length(serum_cols_clean) ) } -serum_cols_to_extract = c(meta_data_cols, serum_cols_clean) +serum_cols_to_extract = c(meta_clinical_cols, serum_cols_clean) cat("Extracting SERUM cols + metadata_cols") -if ( length(serum_cols_to_extract) == length(meta_data_cols) + length(serum_cols_clean) ){ +if ( length(serum_cols_to_extract) == length(meta_clinical_cols) + length(serum_cols_clean) ){ cat("Extracing", length(serum_cols_to_extract), "columns for serum") serum_df = my_data[, serum_cols_to_extract] }else{ cat("FAIL: length mismatch" - , "Expeceted to extract:", length(meta_data_cols) + length(serum_cols_clean), "columns" + , "Expeceted to extract:", length(meta_clinical_cols) + length(serum_cols_clean), "columns" , "Got:", length(serum_cols_to_extract)) } @@ -130,16 +130,16 @@ if( length(npa_cols_clean) == length(npa_cols) - length(npa_cols_to_omit) ){ , "Got:", length(npa_cols_clean) ) } -npa_cols_to_extract = c(meta_data_cols, npa_cols_clean) +npa_cols_to_extract = c(meta_clinical_cols, npa_cols_clean) cat("Extracting NPA cols + metadata_cols") -if ( length(npa_cols_to_extract) == length(meta_data_cols) + length(npa_cols_clean) ){ +if ( length(npa_cols_to_extract) == length(meta_clinical_cols) + length(npa_cols_clean) ){ cat("Extracing", length(npa_cols_to_extract), "columns for npa") npa_df = my_data[, npa_cols_to_extract] }else{ cat("FAIL: length mismatch" - , "Expeceted to extract:", length(meta_data_cols) + length(npa_cols_clean), "columns" + , "Expeceted to extract:", length(meta_clinical_cols) + length(npa_cols_clean), "columns" , "Got:", length(npa_cols_to_extract)) } @@ -184,11 +184,11 @@ cols_to_omit = c("adult" #, "weight_unit", "visual_est_bmi", "bmi_rating" ) -pivot_cols = meta_data_cols +pivot_cols = meta_clinical_cols # subselect pivot_cols -pivot_cols = meta_data_cols[!meta_data_cols%in%cols_to_omit];pivot_cols -ncols_omitted = table(meta_data_cols%in%cols_to_omit)[[2]] +pivot_cols = meta_clinical_cols[!meta_clinical_cols%in%cols_to_omit];pivot_cols +ncols_omitted = table(meta_clinical_cols%in%cols_to_omit)[[2]] ncols_omitted #============== @@ -203,16 +203,16 @@ sam_df_adults = sam_df wf_cols = colnames(sam_df_adults)[!colnames(sam_df_adults)%in%cols_to_omit] sam_wf = sam_df_adults[wf_cols] -pivot_cols = meta_data_cols +pivot_cols = meta_clinical_cols # subselect pivot_cols -pivot_cols = meta_data_cols[!meta_data_cols%in%cols_to_omit];pivot_cols +pivot_cols = meta_clinical_cols[!meta_clinical_cols%in%cols_to_omit];pivot_cols -if (length(pivot_cols) == length(meta_data_cols) - ncols_omitted){ +if (length(pivot_cols) == length(meta_clinical_cols) - ncols_omitted){ cat("PASS: pivot cols successfully extracted") }else{ cat("FAIL: length mismatch! pivot cols could not be extracted" - , "\nExpected length:", length(meta_data_cols) - ncols_omitted + , "\nExpected length:", length(meta_clinical_cols) - ncols_omitted , "\nGot:",length(pivot_cols) ) quit() } @@ -256,14 +256,14 @@ serum_df_adults = serum_df wf_cols = colnames(serum_df_adults)[!colnames(serum_df_adults)%in%cols_to_omit] serum_wf = serum_df_adults[wf_cols] -pivot_cols = meta_data_cols -pivot_cols = meta_data_cols[!meta_data_cols%in%cols_to_omit];pivot_cols +pivot_cols = meta_clinical_cols +pivot_cols = meta_clinical_cols[!meta_clinical_cols%in%cols_to_omit];pivot_cols -if (length(pivot_cols) == length(meta_data_cols) - ncols_omitted){ +if (length(pivot_cols) == length(meta_clinical_cols) - ncols_omitted){ cat("PASS: pivot cols successfully extracted") }else{ cat("FAIL: length mismatch! pivot cols could not be extracted" - , "\nExpected length:", length(meta_data_cols) - ncols_omitted + , "\nExpected length:", length(meta_clinical_cols) - ncols_omitted , "\nGot:",length(pivot_cols) ) quit() } @@ -303,14 +303,14 @@ npa_df_adults = npa_df wf_cols = colnames(npa_df_adults)[!colnames(npa_df_adults)%in%cols_to_omit] npa_wf = npa_df_adults[wf_cols] -pivot_cols = meta_data_cols -pivot_cols = meta_data_cols[!meta_data_cols%in%cols_to_omit];pivot_cols +pivot_cols = meta_clinical_cols +pivot_cols = meta_clinical_cols[!meta_clinical_cols%in%cols_to_omit];pivot_cols -if (length(pivot_cols) == length(meta_data_cols) - ncols_omitted){ +if (length(pivot_cols) == length(meta_clinical_cols) - ncols_omitted){ cat("PASS: pivot cols successfully extracted") }else{ cat("FAIL: length mismatch! pivot cols could not be extracted" - , "\nExpected length:", length(meta_data_cols) - ncols_omitted + , "\nExpected length:", length(meta_clinical_cols) - ncols_omitted , "\nGot:",length(pivot_cols) ) quit() }