# PROCESSING ----------------------------------------------------------------------------------------------------------
#
calc_phospho_enrichment_efficiency <- function(filtered.data)
{
total.tags <- sum(filtered.data$"Phospho (STY)")
at.least.one.tag <- sum(filtered.data$"Phospho (STY)" >= 1)
one.tag <- sum(filtered.data$"Phospho (STY)" == 1)
two.tags <- sum(filtered.data$"Phospho (STY)" == 2)
three.tags <- sum(filtered.data$"Phospho (STY)" == 3)
four.or.more.tags <- sum(filtered.data$"Phospho (STY)" >= 4)
no.sites <- sum(filtered.data$"Phospho (STY)" == 0)
multiple.tags <- total.tags - at.least.one.tag
phospho.enrichment.calculations <- tibble("Total Phospho Sites" = total.tags,
"At Least 1 Site" = at.least.one.tag,
"1 Site" = one.tag,
"2 Sites" = two.tags,
"3 Sites" = three.tags,
"4 Sites or More" = four.or.more.tags,
"No Sites" = no.sites,
"Tagged Multiple Sites" = multiple.tags)
#
phospho.enrichment.calculations
}
calc_phospho_localized <- function(filtered.data)
{
total <- nrow(filtered.data)
localized.data <- subset(filtered.data, filtered.data$"Localization prob" >= .75)
serine <- sum(localized.data$"Amino acid" == "S")
threonine <- sum(localized.data$"Amino acid" == "T")
tyrosine <- sum(localized.data$"Amino acid" == "Y")
totalabovepercent <- nrow(localized.data)
localized_phosph_data <- tibble("Total" = total,
"Total Phospho Sites Above 75% Localization" = totalabovepercent,
"Serine" = serine,
"% S" = (serine/totalabovepercent)*100,
"Threonine" = threonine,
"% T" = (threonine/totalabovepercent)*100,
"Tyrosine" = tyrosine,
"% Y" = (tyrosine/totalabovepercent)*100)
}
calc_phospho_fractions <- function(filtered.data)
{
fractions <- grep("Localization prob ", colnames(filtered.data), ignore.case = FALSE, perl = FALSE, fixed = FALSE, useBytes = FALSE, value = TRUE)
calc_all_data <- calc_phospho_localized(filtered.data)
calc_all_data$Fraction <- "All"
for (i in fractions)
{
calc_stats_fraction <- subset(filtered.data, filtered.data[[i]] != "NA")
fraction_data <- calc_phospho_localized(calc_stats_fraction)
fraction_data$Fraction <- i
calc_all_data <- rbind(calc_all_data, fraction_data)
}
calc_all_data[, c(ncol(calc_all_data),(seq(2, ncol(calc_all_data)-1)))]
}
# VISUALIZATION -------------------------------------------------------------------------------------------------------
#
plot_phospho_enrichment_efficiency <- function()
{
}
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