From 1562a096310d3616453871a68cae1f67543737cf Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Fri, 20 Nov 2020 12:36:55 +0000 Subject: [PATCH] added quick summary to see sig meds just before writing file --- colnames_clinical_meds.R | 0 data_extraction_formatting_clinical.R | 0 data_extraction_formatting_non_asthmatics.R | 0 data_extraction_formatting_regression.R | 0 flu_stats_unpaired_na_npa.R | 24 +++++++++--------- flu_stats_unpaired_npa.R | 18 ++++++++----- flu_stats_unpaired_sam.R | 22 +++++++++++++--- flu_stats_unpaired_serum.R | 28 +++++++++++++++------ 8 files changed, 63 insertions(+), 29 deletions(-) mode change 100644 => 100755 colnames_clinical_meds.R mode change 100644 => 100755 data_extraction_formatting_clinical.R mode change 100644 => 100755 data_extraction_formatting_non_asthmatics.R mode change 100644 => 100755 data_extraction_formatting_regression.R diff --git a/colnames_clinical_meds.R b/colnames_clinical_meds.R old mode 100644 new mode 100755 diff --git a/data_extraction_formatting_clinical.R b/data_extraction_formatting_clinical.R old mode 100644 new mode 100755 diff --git a/data_extraction_formatting_non_asthmatics.R b/data_extraction_formatting_non_asthmatics.R old mode 100644 new mode 100755 diff --git a/data_extraction_formatting_regression.R b/data_extraction_formatting_regression.R old mode 100644 new mode 100755 diff --git a/flu_stats_unpaired_na_npa.R b/flu_stats_unpaired_na_npa.R index 3322135..3f5d3de 100755 --- a/flu_stats_unpaired_na_npa.R +++ b/flu_stats_unpaired_na_npa.R @@ -43,12 +43,6 @@ rm(pivot_cols) # sanity checks table(lf$timepoint) -#if (table(lf$flustat) == table(npa_lf$flustat)[[2]]){ -# cat("Analysing Flu positive patients for:", my_sample_type) -#}else{ -# cat("FAIL: problem with subsetting data for:", my_sample_type) -# quit() -#} ######################################################################## # Unpaired stats at each timepoint b/w groups: wilcoxon UNpaired analysis # with correction @@ -366,16 +360,22 @@ colnames(combined_unpaired_stats_f) = c("mediator" colnames(combined_unpaired_stats_f) +#--------------- +# quick summary +#--------------- # count how many meds are significant -n_sig = length(combined_unpaired_stats_f$mediator[combined_unpaired_stats_f$p_signif<0.05]) -cat("\nTotal no. of statistically significant mediators in", toupper(my_sample_type) - , "are:", n_sig) +n_sig = length(combined_unpaired_stats_f$mediator[combined_unpaired_stats_f$p_signif<0.05 & !is.na(combined_unpaired_stats_f$p_signif<0.05)]) +sig_meds = combined_unpaired_stats_f[(combined_unpaired_stats_f$p_signif<0.05 & !is.na(combined_unpaired_stats_f$p_signif<0.05)),] -sig_meds = combined_unpaired_stats_f[combined_unpaired_stats_f$p_signif<0.05,] +sig_meds$med_time = paste0(sig_meds$mediator, "@", sig_meds$timepoint) + +cat("\nTotal no. of statistically significant mediators in", toupper(my_sample_type) + , "are:", n_sig + , "\nThese are:", sig_meds$med_time) ######################################################################## #****************** # write output file #****************** -cat("UNpaired stats for groups will be:", flu_stats_time_unpaired_na) -write.csv(combined_unpaired_stats_f, flu_stats_time_unpaired_na, row.names = FALSE) +cat("\nUNpaired stats for groups will be:", flu_stats_time_unpaired_na) +#write.csv(combined_unpaired_stats_f, flu_stats_time_unpaired_na, row.names = FALSE) diff --git a/flu_stats_unpaired_npa.R b/flu_stats_unpaired_npa.R index f302f8f..8750b16 100755 --- a/flu_stats_unpaired_npa.R +++ b/flu_stats_unpaired_npa.R @@ -366,16 +366,22 @@ colnames(combined_unpaired_stats_f) = c("mediator" colnames(combined_unpaired_stats_f) +#--------------- +# quick summary +#--------------- # count how many meds are significant -n_sig = length(combined_unpaired_stats_f$mediator[combined_unpaired_stats_f$p_signif<0.05]) -cat("\nTotal no. of statistically significant mediators in", toupper(my_sample_type) - , "are:", n_sig) +n_sig = length(combined_unpaired_stats_f$mediator[combined_unpaired_stats_f$p_signif<0.05 & !is.na(combined_unpaired_stats_f$p_signif<0.05)]) +sig_meds = combined_unpaired_stats_f[(combined_unpaired_stats_f$p_signif<0.05 & !is.na(combined_unpaired_stats_f$p_signif<0.05)),] -sig_meds = combined_unpaired_stats_f[combined_unpaired_stats_f$p_signif<0.05,] +sig_meds$med_time = paste0(sig_meds$mediator, "@", sig_meds$timepoint) + +cat("\nTotal no. of statistically significant mediators in", toupper(my_sample_type) + , "are:", n_sig + , "\nThese are:", sig_meds$med_time) ######################################################################## #****************** # write output file #****************** -cat("UNpaired stats for groups will be:", flu_stats_time_unpaired) -write.csv(combined_unpaired_stats_f, flu_stats_time_unpaired, row.names = FALSE) +cat("\nUNpaired stats for groups will be:", flu_stats_time_unpaired) +#write.csv(combined_unpaired_stats_f, flu_stats_time_unpaired, row.names = FALSE) diff --git a/flu_stats_unpaired_sam.R b/flu_stats_unpaired_sam.R index 0797766..6327834 100755 --- a/flu_stats_unpaired_sam.R +++ b/flu_stats_unpaired_sam.R @@ -71,8 +71,8 @@ foo = lf_t1[which(is.na(lf_t1$value)),] lf_t1_comp = lf_t1[-which(is.na(lf_t1$value)),] stats_un_t1 = compare_means(value~obesity , group.by = "mediator" - , data = lf_t1 - #, data = lf_t1_comp + #, data = lf_t1 + , data = lf_t1_comp , paired = FALSE , p.adjust.method = my_adjust_method) @@ -368,9 +368,23 @@ colnames(combined_unpaired_stats_f) = c("mediator" , "p_bon_signif") colnames(combined_unpaired_stats_f) + +#--------------- +# quick summary +#--------------- +# count how many meds are significant +n_sig = length(combined_unpaired_stats_f$mediator[combined_unpaired_stats_f$p_signif<0.05 & !is.na(combined_unpaired_stats_f$p_signif<0.05)]) +sig_meds = combined_unpaired_stats_f[(combined_unpaired_stats_f$p_signif<0.05 & !is.na(combined_unpaired_stats_f$p_signif<0.05)),] + +sig_meds$med_time = paste0(sig_meds$mediator, "@", sig_meds$timepoint) + +cat("\nTotal no. of statistically significant mediators in", toupper(my_sample_type) + , "are:", n_sig + , "\nThese are:", sig_meds$med_time) + ####################################################################### #****************** # write output file #****************** -cat("UNpaired stats for groups will be:", flu_stats_time_unpaired) -write.csv(combined_unpaired_stats_f, flu_stats_time_unpaired, row.names = FALSE) +cat("\nUNpaired stats for groups will be:", flu_stats_time_unpaired) +#write.csv(combined_unpaired_stats_f, flu_stats_time_unpaired, row.names = FALSE) diff --git a/flu_stats_unpaired_serum.R b/flu_stats_unpaired_serum.R index a069975..367ba1f 100755 --- a/flu_stats_unpaired_serum.R +++ b/flu_stats_unpaired_serum.R @@ -67,8 +67,8 @@ ci = which(is.na(lf_t1$value)) lf_t1_comp = lf_t1[-which(is.na(lf_t1$value)),] stats_un_t1 = compare_means(value~obesity , group.by = "mediator" - , data = lf_t1 - #, data = lf_t1_comp + #, data = lf_t1 + , data = lf_t1_comp , paired = FALSE , p.adjust.method = my_adjust_method) @@ -129,8 +129,8 @@ lf_t2_comp = lf_t2[-which(is.na(lf_t2$value)),] stats_un_t2 = compare_means(value~obesity , group.by = "mediator" - , data = lf_t2 - #, data = lf_t2_comp + #, data = lf_t2 + , data = lf_t2_comp , paired = FALSE , p.adjust.method = my_adjust_method) # add timepoint and convert to df @@ -188,8 +188,8 @@ lf_t3_comp = lf_t3[-which(is.na(lf_t3$value)),] stats_un_t3 = compare_means(value~obesity , group.by = "mediator" - , data = lf_t3 - #, data = lf_t3_comp + #, data = lf_t3 + , data = lf_t3_comp , paired = FALSE , p.adjust.method = my_adjust_method) @@ -361,9 +361,23 @@ colnames(combined_unpaired_stats_f) = c("mediator" , "p_bon_signif") colnames(combined_unpaired_stats_f) + +#--------------- +# quick summary +#--------------- +# count how many meds are significant +n_sig = length(combined_unpaired_stats_f$mediator[combined_unpaired_stats_f$p_signif<0.05 & !is.na(combined_unpaired_stats_f$p_signif<0.05)]) +sig_meds = combined_unpaired_stats_f[(combined_unpaired_stats_f$p_signif<0.05 & !is.na(combined_unpaired_stats_f$p_signif<0.05)),] + +sig_meds$med_time = paste0(sig_meds$mediator, "@", sig_meds$timepoint) + +cat("\nTotal no. of statistically significant mediators in", toupper(my_sample_type) + , "are:", n_sig + , "\nThese are:", sig_meds$med_time) + ######################################################################## #****************** # write output file #****************** cat("UNpaired stats for groups will be:", flu_stats_time_unpaired) -write.csv(combined_unpaired_stats_f, flu_stats_time_unpaired, row.names = FALSE) +#write.csv(combined_unpaired_stats_f, flu_stats_time_unpaired, row.names = FALSE)