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reformatted to generate outfile_name for flu stats

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Tanushree Tunstall 2020-10-26 16:12:51 +00:00
parent 61fbb2f8d6
commit 6e54f339d1
3 changed files with 17 additions and 13 deletions
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8
flu_stats_unpaired_npa.R
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@ -20,10 +20,12 @@ rm(colnames_sam_df, expected_rows_sam_lf
rm(pivot_cols) rm(pivot_cols)
my_sample_type = "npa"
#============= #=============
# Output: unpaired analysis of time for npa # Output: unpaired analysis of time for npa
#============= #=============
stats_time_unpaired_flu_npa = paste0(outdir_stats, "flu_stats_time_unpaired_npa.csv") outfile_name = paste0("flu_stats_time_unpaired_", my_sample_type, ".csv")
flu_stats_time_unpaired = paste0(outdir_stats, outfile_name)
#%%======================================================== #%%========================================================
# data assignment for stats # data assignment for stats
@ -316,5 +318,5 @@ colnames(combined_unpaired_stats_f)
#****************** #******************
# write output file # write output file
#****************** #******************
cat("UNpaired stats for groups will be:", stats_time_unpaired_flu_npa) cat("UNpaired stats for groups will be:", flu_stats_time_unpaired)
write.csv(combined_unpaired_stats_f, stats_time_unpaired_flu_npa, row.names = FALSE) write.csv(combined_unpaired_stats_f, flu_stats_time_unpaired, row.names = FALSE)

11
flu_stats_unpaired_sam.R
View file

@ -20,10 +20,13 @@ rm(colnames_npa_df, expected_rows_npa_lf
rm(pivot_cols) rm(pivot_cols)
my_sample_type = "sam"
#============= #=============
# Output: unpaired analysis of time for sam # Output: unpaired analysis of time for sam
#============= #=============
stats_time_unpaired_flu_sam = paste0(outdir_stats, "flu_stats_time_unpaired_sam.csv") outfile_name = paste0("flu_stats_time_unpaired_", my_sample_type, ".csv")
flu_stats_time_unpaired = paste0(outdir_stats, outfile_name)
#%%======================================================== #%%========================================================
# data assignment for stats # data assignment for stats
wf = sam_df_adults_clean[sam_df_adults_clean$flustat == 1,] wf = sam_df_adults_clean[sam_df_adults_clean$flustat == 1,]
@ -32,8 +35,6 @@ lf = sam_adults_lf[sam_adults_lf$flustat == 1,]
table(lf$timepoint) table(lf$timepoint)
length(unique(lf$mosaic)) length(unique(lf$mosaic))
lf$timepoint = paste0("t", lf$timepoint) lf$timepoint = paste0("t", lf$timepoint)
my_sample_type = "sam"
######################################################################## ########################################################################
# Unpaired stats at each timepoint b/w groups: wilcoxon UNpaired analysis # Unpaired stats at each timepoint b/w groups: wilcoxon UNpaired analysis
# with correction # with correction
@ -317,5 +318,5 @@ colnames(combined_unpaired_stats_f)
#****************** #******************
# write output file # write output file
#****************** #******************
cat("UNpaired stats for groups will be:", stats_time_unpaired_flu_sam) cat("UNpaired stats for groups will be:", flu_stats_time_unpaired)
write.csv(combined_unpaired_stats_f, stats_time_unpaired_flu_sam, row.names = FALSE) write.csv(combined_unpaired_stats_f, flu_stats_time_unpaired, row.names = FALSE)

11
flu_stats_unpaired_serum.R
View file

@ -20,10 +20,13 @@ rm(colnames_sam_df, expected_rows_sam_lf
rm(pivot_cols) rm(pivot_cols)
my_sample_type = "serum"
#============= #=============
# Output: unpaired analysis of time for serum # Output: unpaired analysis of time for serum
#============= #=============
stats_time_unpaired_flu_serum = paste0(outdir_stats, "flu_stats_time_unpaired_serum.csv") outfile_name = paste0("flu_stats_time_unpaired_", my_sample_type, ".csv")
flu_stats_time_unpaired = paste0(outdir_stats, outfile_name)
#%%======================================================== #%%========================================================
# data assignment for stats # data assignment for stats
wf = serum_df_adults_clean[serum_df_adults_clean$flustat == 1,] wf = serum_df_adults_clean[serum_df_adults_clean$flustat == 1,]
@ -32,8 +35,6 @@ lf = serum_adults_lf[serum_adults_lf$flustat == 1,]
table(lf$timepoint) table(lf$timepoint)
lf$timepoint = paste0("t", lf$timepoint) lf$timepoint = paste0("t", lf$timepoint)
my_sample_type = "serum"
######################################################################## ########################################################################
# Unpaired stats at each timepoint b/w groups: wilcoxon UNpaired analysis with correction # Unpaired stats at each timepoint b/w groups: wilcoxon UNpaired analysis with correction
####################################################################### #######################################################################
@ -315,5 +316,5 @@ colnames(combined_unpaired_stats_f)
#****************** #******************
# write output file # write output file
#****************** #******************
cat("UNpaired stats for groups will be:", stats_time_unpaired_flu_serum) cat("UNpaired stats for groups will be:", flu_stats_time_unpaired)
write.csv(combined_unpaired_stats_f, stats_time_unpaired_flu_serum, row.names = FALSE) write.csv(combined_unpaired_stats_f, flu_stats_time_unpaired, row.names = FALSE)