formatted non-flu stats in the same way as the flu ones
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10 changed files with 319 additions and 226 deletions
107
flu_stats_unpaired_sam.R
Normal file → Executable file
107
flu_stats_unpaired_sam.R
Normal file → Executable file
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@ -32,9 +32,11 @@ lf = sam_adults_lf[sam_adults_lf$flustat == 1,]
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table(lf$timepoint)
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length(unique(lf$mosaic))
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lf$timepoint = paste0("t", lf$timepoint)
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my_sample_type = "sam"
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########################################################################
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# Unpaired stats at each timepoint b/w groups: wilcoxon UNpaired analysis with correction
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# Unpaired stats at each timepoint b/w groups: wilcoxon UNpaired analysis
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# with correction
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#######################################################################
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# with adjustment: fdr and BH are identical
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my_adjust_method = "BH"
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@ -88,6 +90,9 @@ if (all(n_t1$mediator%in%stats_un_t1$mediator)) {
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, "\nncol:", ncol(stats_un_t1))
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}
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# add bonferroni adjustment as well
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stats_un_t1$p_adj_bonferroni = p.adjust(stats_un_t1$p, method = "bonferroni")
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rm(n_t1)
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rm(lf_t1_comp)
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@ -132,8 +137,8 @@ if (all(n_t2$mediator%in%stats_un_t2$mediator)) {
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, "\nncol:", ncol(stats_un_t2))
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}
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# check: satisfied!!!!
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wilcox.test()
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# add bonferroni adjustment as well
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stats_un_t2$p_adj_bonferroni = p.adjust(stats_un_t2$p, method = "bonferroni")
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rm(n_t2)
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rm(lf_t2_comp)
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@ -184,6 +189,9 @@ if (all(n_t3$mediator%in%stats_un_t3$mediator)) {
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# FIXME: supply the col name automatically?
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wilcox.test(wf$ifna2a_sam3[wf$obesity == 1], wf$ifna2a_sam3[wf$obesity == 0])
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# add bonferroni adjustment as well
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stats_un_t3$p_adj_bonferroni = p.adjust(stats_un_t3$p, method = "bonferroni")
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rm(n_t3)
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rm(lf_t3_comp)
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@ -223,46 +231,41 @@ if ( nrow(combined_unpaired_stats) == expected_rows && ncol(combined_unpaired_st
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quit()
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}
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#===============================================================
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#######################################################################
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#=================
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# formatting df
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# delete unnecessary column
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#=================
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# delete: unnecessary column
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combined_unpaired_stats = subset(combined_unpaired_stats, select = -c(.y.))
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# reflect stats method correctly
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combined_unpaired_stats$method
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# add sample_type
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cat("Adding sample type info as a column", my_sample_type, "...")
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combined_unpaired_stats$sample_type = my_sample_type
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# add: reflect stats method correctly i.e paired or unpaired
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# incase there are NA due to LLODs, the gsub won't work!
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#combined_unpaired_stats$method = gsub("Wilcoxon", "Wilcoxon_unpaired", combined_unpaired_stats$method)
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combined_unpaired_stats$method = "wilcoxon unpaired"
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combined_unpaired_stats$method
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# replace "." in colnames with "_"
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colnames(combined_unpaired_stats)
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#names(combined_unpaired_stats) = gsub("\.", "_", names(combined_unpaired_stats)) # weird!!!!
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colnames(combined_unpaired_stats) = c("mediator"
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, "group1"
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, "group2"
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, "p"
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, "p_adj"
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, "p_format"
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, "p_signif"
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, "method"
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, "timepoint"
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, "n_obs")
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colnames(combined_unpaired_stats)
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combined_unpaired_stats$sample_type = "sam"
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# add an extra column for padjust_signif
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combined_unpaired_stats$padjust_signif = round(combined_unpaired_stats$p_adj, digits = 2)
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# add appropriate symbols for padjust_signif
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# add an extra column for padjust_signif: my_adjust_method
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combined_unpaired_stats$padjust_signif = combined_unpaired_stats$p.adj
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# add appropriate symbols for padjust_signif: my_adjust_method
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combined_unpaired_stats = dplyr::mutate(combined_unpaired_stats, padjust_signif = case_when(padjust_signif == 0.05 ~ "."
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, padjust_signif <=0.0001 ~ '****'
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, padjust_signif <=0.001 ~ '***'
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, padjust_signif <=0.01 ~ '**'
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, padjust_signif <0.05 ~ '*'
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, TRUE ~ 'ns'))
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, padjust_signif <=0.0001 ~ '****'
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, padjust_signif <=0.001 ~ '***'
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, padjust_signif <=0.01 ~ '**'
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, padjust_signif <0.05 ~ '*'
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, TRUE ~ 'ns'))
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# add an extra column for p_bon_signif
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combined_unpaired_stats$p_bon_signif = combined_unpaired_stats$p_adj_bonferroni
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# add appropriate symbols for p_bon_signif
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combined_unpaired_stats = dplyr::mutate(combined_unpaired_stats, p_bon_signif = case_when(p_bon_signif == 0.05 ~ "."
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, p_bon_signif <=0.0001 ~ '****'
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, p_bon_signif <=0.001 ~ '***'
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, p_bon_signif <=0.01 ~ '**'
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, p_bon_signif <0.05 ~ '*'
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, TRUE ~ 'ns'))
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# reorder columns
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print("preparing to reorder columns...")
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colnames(combined_unpaired_stats)
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@ -274,16 +277,18 @@ my_col_order2 = c("mediator"
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, "group2"
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, "method"
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, "p"
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, "p_format"
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, "p_signif"
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, "p_adj"
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, "padjust_signif")
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, "p.format"
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, "p.signif"
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, "p.adj"
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, "padjust_signif"
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, "p_adj_bonferroni"
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, "p_bon_signif")
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if( length(my_col_order2) == ncol(combined_unpaired_stats) && all(my_col_order2%in%colnames(combined_unpaired_stats)) ){
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if( length(my_col_order2) == ncol(combined_unpaired_stats) && (all(my_col_order2%in%colnames(combined_unpaired_stats))) ){
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print("PASS: Reordering columns...")
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combined_unpaired_stats_f = combined_unpaired_stats[, my_col_order2]
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print("Successful: column reordering")
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print("formatted df called:'combined_unpaired_stats_f'")
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print("formatted df called:'combined_unpaired_stats_f'")
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cat('\nformatted df has the following dimensions\n')
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print(dim(combined_unpaired_stats_f ))
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} else{
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@ -291,10 +296,26 @@ if( length(my_col_order2) == ncol(combined_unpaired_stats) && all(my_col_order2%
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, "\nExpected column order for: ", ncol(combined_unpaired_stats)
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, "\nGot:", length(my_col_order2)))
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quit()
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}
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}
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# assign nice column names like replace "." with "_"
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colnames(combined_unpaired_stats_f) = c("mediator"
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, "timepoint"
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, "sample_type"
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, "n_obs"
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, "group1"
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, "group2"
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, "method"
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, "p"
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, "p_format"
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, "p_signif"
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, paste0("p_adj_fdr_", my_adjust_method)
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, paste0("p_", my_adjust_method, "_signif")
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, "p_adj_bonferroni"
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, "p_bon_signif")
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colnames(combined_unpaired_stats_f)
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#******************
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# write output file
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#******************
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cat("UNpaired stats for groups will be:", stats_time_unpaired_flu_sam)
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write.csv(combined_unpaired_stats_f, stats_time_unpaired_flu_sam, row.names = FALSE)
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write.csv(combined_unpaired_stats_f, stats_time_unpaired_flu_sam, row.names = FALSE)
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