Commit d51bf434 authored by domingue's avatar domingue

Included more detailed information about proteins missing

parent 864d332b
......@@ -590,6 +590,29 @@ sig_tab <- df_wide %>%
] %>%
dcast(ID + name + contrast ~ stat)
## Number of NAs per condition:
table_nas <- assay(data_se) %>%
as_df() %>%
rownames_to_column("name") %>%
gather(label, intensity, -name) %>%
left_join(experimental_design) %>%
group_by(name, condition) %>%
summarise(
num_NAs = sum(is.na(intensity)),
percent_NAs = num_NAs / length(unique(label)) * 100
) %>%
ungroup() %>%
inner_join(., ., by = "name", suffix = c("_1", "_2")) %>%
rename(
condition_1 = "condition",
condition_2 = "control",
num_NAs_1 = "num_NAs_condition",
num_NAs_2 = "num_NAs_control",
percent_NAs_1 = "percent_NAs_condition",
percent_NAs_2 = "percent_NAs_control"
)
## assemble table with results
dep_results <- stats_tab %>%
left_join(sig_tab) %>%
mutate(
......@@ -601,7 +624,8 @@ dep_results <- stats_tab %>%
) %>%
left_join(cond_means) %>%
left_join(all_means) %>%
left_join(protein_info)
left_join(protein_info) %>%
left_join(table_nas)
## export intensities used for the differential expression analysis
......
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