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ran scripts to check

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This commit is contained in:
Tanushree Tunstall 2020-10-29 13:20:51 +00:00
parent 1e6e9eaef1
commit e1f97df805
3 changed files with 2 additions and 4 deletions
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2
flu_stats_unpaired_npa.R
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@ -61,7 +61,7 @@ my_adjust_method = "BH"
lf_t1 = lf[lf$timepoint == "t1",] lf_t1 = lf[lf$timepoint == "t1",]
sum(is.na(lf_t1$value)) sum(is.na(lf_t1$value))
#foo = lf_t1[which(is.na(lf_t1$value)),] foo = lf_t1[which(is.na(lf_t1$value)),]
#ci = which(is.na(lf_t1$value)) #ci = which(is.na(lf_t1$value))
#lf_t1_comp = lf_t1[-ci,] #lf_t1_comp = lf_t1[-ci,]

3
flu_stats_unpaired_sam.R
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@ -42,7 +42,6 @@ rm(pivot_cols)
# sanity checks # sanity checks
table(lf$timepoint) table(lf$timepoint)
length(unique(lf$mosaic)) length(unique(lf$mosaic))
lf$timepoint = paste0("t", lf$timepoint)
if (table(lf$flustat) == table(sam_lf$flustat)[[2]]){ if (table(lf$flustat) == table(sam_lf$flustat)[[2]]){
cat("Analysing Flu positive patients for:", my_sample_type) cat("Analysing Flu positive patients for:", my_sample_type)
@ -64,7 +63,7 @@ my_adjust_method = "BH"
lf_t1 = lf[lf$timepoint == "t1",] lf_t1 = lf[lf$timepoint == "t1",]
sum(is.na(lf_t1$value)) sum(is.na(lf_t1$value))
#foo = lf_t1[which(is.na(lf_t1$value)),] foo = lf_t1[which(is.na(lf_t1$value)),]
#ci = which(is.na(lf_t1$value)) #ci = which(is.na(lf_t1$value))
#lf_t1_comp = lf_t1[-ci,] #lf_t1_comp = lf_t1[-ci,]

1
flu_stats_unpaired_serum.R
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@ -39,7 +39,6 @@ rm(pivot_cols)
# sanity checks # sanity checks
table(lf$timepoint) table(lf$timepoint)
lf$timepoint = paste0("t", lf$timepoint)
if (table(lf$flustat) == table(serum_lf$flustat)[[2]]){ if (table(lf$flustat) == table(serum_lf$flustat)[[2]]){
cat("Analysing Flu positive patients for:", my_sample_type) cat("Analysing Flu positive patients for:", my_sample_type)