390 lines
15 KiB
R
Executable file
390 lines
15 KiB
R
Executable file
#!/usr/bin/Rscript
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getwd()
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setwd("~/git/mosaic_2020/")
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getwd()
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############################################################
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# TASK: unpaired (time) analysis of mediators:
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# sample type: SAM
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# data: Flu positive adult patients
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# group: obesity
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############################################################
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my_sample_type = "sam"
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#=============
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# Input
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#=============
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source("data_extraction_mediators.R")
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# check: adult variable and age variable discrepancy!
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metadata_all$mosaic[metadata_all$adult==1 & metadata_all$age<=18]
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#=============
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# Output
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#=============
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outfile_name = paste0("flu_stats_time_unpaired_", my_sample_type, ".csv")
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flu_stats_time_unpaired = paste0(outdir_stats, outfile_name)
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#===============================
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# data assignment for stats
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#================================
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wf = sam_wf[sam_wf$flustat == 1,]
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lf = sam_lf[sam_lf$flustat == 1,]
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lf$timepoint = paste0("t", lf$timepoint)
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lf = lf[!lf$mediator == "vitd",]
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########################################################################
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# clear variables
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rm(npa_lf, npa_wf
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, serum_lf, serum_wf)
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rm(colnames_npa_df, expected_rows_npa_lf
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, colnames_serum_df, expected_rows_serum_lf)
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rm(pivot_cols)
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# sanity checks
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table(lf$timepoint)
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length(unique(lf$mosaic))
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#if (table(lf$flustat) == table(sam_lf$flustat)[[2]]){
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# cat("Analysing Flu positive patients for:", my_sample_type)
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#}else{
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# cat("FAIL: problem with subsetting data for:", my_sample_type)
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# quit()
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#}
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########################################################################
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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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#==============
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# unpaired: t1
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#==============
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lf_t1 = lf[lf$timepoint == "t1",]
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sum(is.na(lf_t1$value))
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foo = lf_t1[which(is.na(lf_t1$value)),]
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#ci = which(is.na(lf_t1$value))
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#lf_t1_comp = lf_t1[-ci,]
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lf_t1_comp = lf_t1[-which(is.na(lf_t1$value)),]
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stats_un_t1 = compare_means(value~obesity
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, group.by = "mediator"
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#, data = lf_t1
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, data = lf_t1_comp
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, paired = FALSE
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, p.adjust.method = my_adjust_method)
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foo$mosaic[!unique(foo$mosaic)%in%unique(lf_t1_comp$mosaic)]
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# add timepoint and convert to df
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stats_un_t1$timepoint = "t1"
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stats_un_t1 = as.data.frame(stats_un_t1)
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class(stats_un_t1)
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#----------------------------------------
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# calculate n_obs for each mediator: t1
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#----------------------------------------
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#n_t1 = data.frame(table(lf_t1_comp$mediator))
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n_t1_all = data.frame(table(lf_t1$mediator))
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colnames(n_t1_all) = c("mediator", "n_obs")
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n_t1_all$mediator = as.character(n_t1_all$mediator)
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n_t1_comp = data.frame(table(lf_t1_comp$mediator))
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colnames(n_t1_comp) = c("mediator", "n_obs_complete")
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n_t1_comp$mediator = as.character(n_t1_comp$mediator)
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merge_cols = intersect(names(n_t1_all), names(n_t1_comp)); merge_cols
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n_t1= merge(n_t1_all, n_t1_comp, by = merge_cols, all = T)
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#==================================
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# Merge: merge stats + n_obs df
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#===================================
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merging_cols = intersect(names(stats_un_t1), names(n_t1)); merging_cols
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if (all(n_t1$mediator%in%stats_un_t1$mediator)) {
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cat("PASS: merging stats and n_obs on column/s:", merging_cols)
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stats_un_t1 = merge(stats_un_t1, n_t1, by = merging_cols, all = T)
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cat("\nsuccessfull merge:"
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, "\nnrow:", nrow(stats_un_t1)
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, "\nncol:", ncol(stats_un_t1))
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}else{
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nf = n_t1$mediator[!n_t1$mediator%in%stats_un_t1$mediator]
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stats_un_t1 = merge(stats_un_t1, n_t1, by = merging_cols, all.y = T)
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cat("\nMerged with caution:"
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, "\nnrows mismatch:", nf
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, "not found in stats possibly due to all obs being LLODs"
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, "\nintroduced NAs for:", nf
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, "\nnrow:", nrow(stats_un_t1)
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, "\nncol:", ncol(stats_un_t1))
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}
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# add bonferroni adjustment as well
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stats_un_t1$p_adj_bonferroni = p.adjust(stats_un_t1$p, method = "bonferroni")
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rm(n_t1)
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rm(lf_t1_comp)
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#==============
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# unpaired: t2
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#==============
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lf_t2 = lf[lf$timepoint == "t2",]
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lf_t2_comp = lf_t2[-which(is.na(lf_t2$value)),]
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stats_un_t2 = compare_means(value~obesity
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, group.by = "mediator"
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#, data = lf_t2
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, data = lf_t2_comp
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, paired = FALSE
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, p.adjust.method = my_adjust_method)
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# add timepoint and convert to df
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stats_un_t2$timepoint = "t2"
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stats_un_t2 = as.data.frame(stats_un_t2)
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class(stats_un_t2)
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#----------------------------------------
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# calculate n_obs for each mediator: t2
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#----------------------------------------
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#n_t2 = data.frame(table(lf_t2_comp$mediator))
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n_t2_all = data.frame(table(lf_t2$mediator))
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colnames(n_t2_all) = c("mediator", "n_obs")
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n_t2_all$mediator = as.character(n_t2_all$mediator)
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n_t2_comp = data.frame(table(lf_t2_comp$mediator))
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colnames(n_t2_comp) = c("mediator", "n_obs_complete")
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n_t2_comp$mediator = as.character(n_t2_comp$mediator)
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merge_cols = intersect(names(n_t2_all), names(n_t2_comp)); merge_cols
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n_t2= merge(n_t2_all, n_t2_comp, by = merge_cols, all = T)
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#==================================
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# Merge: merge stats + n_obs df
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#===================================
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merging_cols = intersect(names(stats_un_t2), names(n_t2)); merging_cols
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if (all(n_t2$mediator%in%stats_un_t2$mediator)) {
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cat("PASS: merging stats and n_obs on column/s:", merging_cols)
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stats_un_t2 = merge(stats_un_t2, n_t2, by = merging_cols, all = T)
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cat("\nsuccessfull merge:"
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, "\nnrow:", nrow(stats_un_t2)
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, "\nncol:", ncol(stats_un_t2))
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}else{
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nf = n_t2$mediator[!n_t2$mediator%in%stats_un_t2$mediator]
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stats_un_t2 = merge(stats_un_t2, n_t2, by = merging_cols, all.y = T)
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cat("\nMerged with caution:"
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, "\nnrows mismatch:", nf
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, "not found in stats possibly due to all obs being LLODs"
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, "\nintroduced NAs for:", nf
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, "\nnrow:", nrow(stats_un_t2)
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, "\nncol:", ncol(stats_un_t2))
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}
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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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#==============
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# unpaired: t3
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#==============
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lf_t3 = lf[lf$timepoint == "t3",]
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lf_t3_comp = lf_t3[-which(is.na(lf_t3$value)),]
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stats_un_t3 = compare_means(value~obesity
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, group.by = "mediator"
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#, data = lf_t3
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, data = lf_t3_comp
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, paired = FALSE
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, p.adjust.method = my_adjust_method)
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# add timepoint and convert to df
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stats_un_t3$timepoint = "t3"
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stats_un_t3 = as.data.frame(stats_un_t3)
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class(stats_un_t3)
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#----------------------------------------
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# calculate n_obs for each mediator: t3
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#----------------------------------------
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#n_t3 = data.frame(table(lf_t3_comp$mediator))
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n_t3_all = data.frame(table(lf_t3$mediator))
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colnames(n_t3_all) = c("mediator", "n_obs")
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n_t3_all$mediator = as.character(n_t3_all$mediator)
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n_t3_comp = data.frame(table(lf_t3_comp$mediator))
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colnames(n_t3_comp) = c("mediator", "n_obs_complete")
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n_t3_comp$mediator = as.character(n_t3_comp$mediator)
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merge_cols = intersect(names(n_t3_all), names(n_t3_comp)); merge_cols
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n_t3= merge(n_t3_all, n_t3_comp, by = merge_cols, all = T)
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#==================================
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# Merge: merge stats + n_obs df
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#==================================
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merging_cols = intersect(names(stats_un_t3), names(n_t3)); merging_cols
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if (all(n_t3$mediator%in%stats_un_t3$mediator)) {
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cat("PASS: merging stats and n_obs on column/s:", merging_cols)
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stats_un_t3 = merge(stats_un_t3, n_t3, by = merging_cols, all = T)
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cat("\nsuccessfull merge:"
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, "\nnrow:", nrow(stats_un_t3)
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, "\nncol:", ncol(stats_un_t3))
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}else{
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nf = n_t3$mediator[!n_t3$mediator%in%stats_un_t3$mediator]
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stats_un_t3 = merge(stats_un_t3, n_t3, by = merging_cols, all.y = T)
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cat("\nMerged with caution:"
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, "\nnrows mismatch:", nf
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, "not found in stats possibly due to all obs being LLODs"
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, "\nintroduced NAs for:", nf
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, "\nnrow:", nrow(stats_un_t3)
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, "\nncol:", ncol(stats_un_t3))
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}
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# check: satisfied!!!!
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# FIXME: supply the col name automatically?
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wilcox.test(wf$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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########################################################################
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#=================
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# Rbind these dfs
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#=================
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str(stats_un_t1);str(stats_un_t2); str(stats_un_t3)
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n_dfs = 3
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if ( all.equal(nrow(stats_un_t1), nrow(stats_un_t2), nrow(stats_un_t3)) &&
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all.equal(ncol(stats_un_t1), ncol(stats_un_t2), ncol(stats_un_t3)) ) {
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expected_rows = nrow(stats_un_t1) * n_dfs
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expected_cols = ncol(stats_un_t1)
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print("PASS: expected_rows and cols variables generated for downstream sanity checks")
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}else{
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cat("FAIL: dfs have different no. of rows and cols"
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, "\nCheck harcoded value of n_dfs"
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, "\nexpected_rows and cols could not be generated")
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quit()
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}
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if ( all.equal(colnames(stats_un_t1), colnames(stats_un_t2), colnames(stats_un_t3)) ){
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print("PASS: colnames match. Rbind the 3 dfs...")
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combined_unpaired_stats = rbind(stats_un_t1, stats_un_t2, stats_un_t3)
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} else{
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cat("FAIL: cannot combined dfs. Colnames don't match!")
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quit()
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}
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if ( nrow(combined_unpaired_stats) == expected_rows && ncol(combined_unpaired_stats) == expected_cols ){
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cat("PASS: combined_df has expected dimension"
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, "\nNo. of rows in combined_df:", nrow(combined_unpaired_stats)
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, "\nNo. of cols in combined_df:", ncol(combined_unpaired_stats) )
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}else{
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cat("FAIL: combined_df dimension mismatch")
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quit()
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}
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#######################################################################
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#=================
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# formatting df
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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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# 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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# 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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# 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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my_col_order2 = c("mediator"
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, "timepoint"
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, "sample_type"
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, "n_obs"
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, "n_obs_complete"
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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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, "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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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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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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cat(paste0("FAIL:Cannot reorder columns, length mismatch"
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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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# 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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, "n_obs_complete"
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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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# quick summary
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#---------------
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# count how many meds are significant
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n_sig = length(combined_unpaired_stats_f$mediator[combined_unpaired_stats_f$p_signif<0.05 & !is.na(combined_unpaired_stats_f$p_signif<0.05)])
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sig_meds = combined_unpaired_stats_f[(combined_unpaired_stats_f$p_signif<0.05 & !is.na(combined_unpaired_stats_f$p_signif<0.05)),]
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sig_meds$med_time = paste0(sig_meds$mediator, "@", sig_meds$timepoint)
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cat("\nTotal no. of statistically significant mediators in", toupper(my_sample_type)
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, "are:", n_sig
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, "\nThese are:", sig_meds$med_time)
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#######################################################################
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#******************
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# write output file
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#******************
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cat("\nUNpaired stats for groups will be:", flu_stats_time_unpaired)
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#write.csv(combined_unpaired_stats_f, flu_stats_time_unpaired, row.names = FALSE)
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