tanu/mosaic_2020
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

separated checks from flu stats and added bonferrroni p

Browse source
This commit is contained in:
Tanushree Tunstall 2020-10-26 13:52:15 +00:00
parent 8e06f382c0
commit fe382dbf89
2 changed files with 62 additions and 47 deletions
Download patch file Download diff file Expand all files Collapse all files

4
read_data.R
View file

@ -12,10 +12,10 @@ maindir = "~/git/mosaic_2020/"
outdir = paste0(maindir, "output/")
ifelse(!dir.exists(outdir), dir.create(outdir), FALSE)
outdir_stats = "~/git/mosaic_2020/output/stats/"
outdir_stats = paste0(maindir, "output/stats/")
ifelse(!dir.exists(outdir_stats), dir.create(outdir_stats), FALSE)
outdir_plots = "~/git/mosaic_2020/output/plots/"
outdir_plots = paste0(maindir, "output/plots")
ifelse(!dir.exists(outdir_plots), dir.create(outdir_plots), FALSE)
########################################################################
# static file read: csv

89
stats_unpaired_flu_npa.R
View file

@ -24,6 +24,7 @@ rm(pivot_cols)
# Output: unpaired analysis of time for npa
#=============
stats_time_unpaired_flu_npa = paste0(outdir_stats, "flu_stats_time_unpaired_npa.csv")
#%%========================================================
# data assignment for stats
wf = npa_df_adults_clean[npa_df_adults_clean$flustat == 1,]
@ -87,8 +88,8 @@ if (all(n_t1$mediator%in%stats_un_t1$mediator)) {
, "\nncol:", ncol(stats_un_t1))
}
# check: satisfied!!!!
wilcox.test()
# add bonferroni adjustment as well
stats_un_t1$p_adj_bonferroni = p.adjust(stats_un_t1$p, method = "bonferroni")
rm(n_t1)
rm(lf_t1_comp)
@ -134,8 +135,8 @@ if (all(n_t2$mediator%in%stats_un_t2$mediator)) {
, "\nncol:", ncol(stats_un_t2))
}
# check: satisfied!!!!
wilcox.test()
# add bonferroni adjustment as well
stats_un_t2$p_adj_bonferroni = p.adjust(stats_un_t2$p, method = "bonferroni")
rm(n_t2)
rm(lf_t2_comp)
@ -182,12 +183,13 @@ if (all(n_t3$mediator%in%stats_un_t3$mediator)) {
, "\nncol:", ncol(stats_un_t3))
}
# check: satisfied!!!!
wilcox.test()
# add bonferroni adjustment as well
stats_un_t3$p_adj_bonferroni = p.adjust(stats_un_t3$p, method = "bonferroni")
rm(n_t3)
rm(lf_t3_comp)
###########################################################################################
#==============
# Rbind these dfs
#==============
@ -224,46 +226,40 @@ if ( nrow(combined_unpaired_stats) == expected_rows && ncol(combined_unpaired_st
quit()
}
#===============================================================
#######################################################################
#=================
# formatting df
# delete unnecessary column
#=================
# delete: unnecessary column
combined_unpaired_stats = subset(combined_unpaired_stats, select = -c(.y.))
# reflect stats method correctly
combined_unpaired_stats$method
# add sample_type
combined_unpaired_stats$sample_type = "npa"
# add: reflect stats method correctly i.e paired or unpaired
# incase there are NA due to LLODs, the gsub won't work!
#combined_unpaired_stats$method = gsub("Wilcoxon", "Wilcoxon_unpaired", combined_unpaired_stats$method)
combined_unpaired_stats$method = "wilcoxon unpaired"
combined_unpaired_stats$method
# replace "." in colnames with "_"
colnames(combined_unpaired_stats)
#names(combined_unpaired_stats) = gsub("\.", "_", names(combined_unpaired_stats)) # weird!!!!
colnames(combined_unpaired_stats) = c("mediator"
, "group1"
, "group2"
, "p"
, "p_adj"
, "p_format"
, "p_signif"
, "method"
, "timepoint"
, "n_obs")
colnames(combined_unpaired_stats)
combined_unpaired_stats$sample_type = "npa"
# add an extra column for padjust_signif
combined_unpaired_stats$padjust_signif = round(combined_unpaired_stats$p_adj, digits = 2)
# add appropriate symbols for padjust_signif
# add an extra column for padjust_signif: my_adjust_method
combined_unpaired_stats$padjust_signif = combined_unpaired_stats$p.adj
# add appropriate symbols for padjust_signif: my_adjust_method
combined_unpaired_stats = dplyr::mutate(combined_unpaired_stats, padjust_signif = case_when(padjust_signif == 0.05 ~ "."
, padjust_signif <=0.0001 ~ '****'
, padjust_signif <=0.001 ~ '***'
, padjust_signif <=0.01 ~ '**'
, padjust_signif <0.05 ~ '*'
, TRUE ~ 'ns'))
# add an extra column for p_bon_signif
combined_unpaired_stats$p_bon_signif = combined_unpaired_stats$p_adj_bonferroni
# add appropriate symbols for p_bon_signif
combined_unpaired_stats = dplyr::mutate(combined_unpaired_stats, p_bon_signif = case_when(p_bon_signif == 0.05 ~ "."
, p_bon_signif <=0.0001 ~ '****'
, p_bon_signif <=0.001 ~ '***'
, p_bon_signif <=0.01 ~ '**'
, p_bon_signif <0.05 ~ '*'
, TRUE ~ 'ns'))
# reorder columns
print("preparing to reorder columns...")
colnames(combined_unpaired_stats)
@ -275,10 +271,12 @@ my_col_order2 = c("mediator"
, "group2"
, "method"
, "p"
, "p_format"
, "p_signif"
, "p_adj"
, "padjust_signif")
, "p.format"
, "p.signif"
, "p.adj"
, "padjust_signif"
, "p_adj_bonferroni"
, "p_bon_signif")
if( length(my_col_order2) == ncol(combined_unpaired_stats) && (all(my_col_order2%in%colnames(combined_unpaired_stats))) ){
print("PASS: Reordering columns...")
@ -293,6 +291,23 @@ if( length(my_col_order2) == ncol(combined_unpaired_stats) && (all(my_col_order2
, "\nGot:", length(my_col_order2)))
quit()
}
# assign nice column names like replace "." with "_"
colnames(combined_unpaired_stats_f) = c("mediator"
, "timepoint"
, "sample_type"
, "n_obs"
, "group1"
, "group2"
, "method"
, "p"
, "p_format"
, "p_signif"
, paste0("p_adj_fdr_", my_adjust_method)
, paste0("p_", my_adjust_method, "_signif")
, "p_adj_bonferroni"
, "p_bon_signif")
colnames(combined_unpaired_stats_f)
#******************
# write output file