#' The KSEA App Analysis (KSEA Kinase Scores Only)
#'
#' Takes a formatted phoshoproteomics data input and returns just the KSEA kinase scores and statistics
#'
#' @param KSData the Kinase-Substrate dataset uploaded from the file
#' prefaced with "PSP&NetworKIN_"
#' available from github.com/casecpb/KSEA/
#' @param PX the experimental data file formatted as described in the KSEA.Complete() documentation
#' @param NetworKIN a binary input of TRUE or FALSE, indicating whether or not to include NetworKIN predictions;
#' NetworKIN = TRUE means inclusion of NetworKIN predictions
#' @param NetworKIN.cutoff a numeric value between 1 and infinity setting
#' the minimum NetworKIN score (can be left out if NetworKIN = FALSE)
#'
#' @return creates a new data frame in R with all the KSEA kinase scores,
#' along with each one's statistical assessment
#'
#' @references
#' Casado et al. (2013) Sci Signal. 6(268):rs6
#'
#' Hornbeck et al. (2015) Nucleic Acids Res. 43:D512-20
#'
#' Horn et al. (2014) Nature Methods 11(6):603-4
#'
#' @examples
#' scores = KSEA.Scores(KSData, PX, NetworKIN=TRUE, NetworKIN.cutoff=3)
#' scores = KSEA.Scores(KSData, PX, NetworKIN=FALSE)
#'
#' @importFrom grDevices dev.off png tiff
#' @importFrom graphics barplot par
#' @importFrom stats aggregate complete.cases p.adjust pnorm sd
#' @importFrom utils write.csv
#'
#' @export
#----------------------------#
# IMPORTANT OVERVIEW OF PX INPUT REQUIREMENTS
# PX input requirements:
# must have exact 6 columns in the following order: Protein, Gene, Peptide, Residue.Both, p, FC
# cannot have NA values, or else the entire peptide row is deleted
# Description of each column in PX:
# - Protein = the Uniprot ID for the parent protein
# - Gene = the HUGO gene name for the parent protein
# - Peptide = the peptide sequence
# - Residue.Both = all phosphosites from that peptide, separated by semicolons if applicable; must be formatted as the single amino acid abbrev. with the residue position (e.g. S102)
# - p = the p-value of that peptide (if none calculated, please write "NULL", cannot be NA)
# - FC = the fold change (not log-transformed); usually recommended to have the control sample as the denominator
#----------------------------#
KSEA.Scores = function (KSData, PX, NetworKIN, NetworKIN.cutoff){
#@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@#
# Process the input data files
#@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@#
#--------------
# Process the PX data file
# Check if each peptide row has multiple phosphorylated residues and create new dataframe with a single residue per row
if (length(grep(";", PX$Residue.Both))==0){
new = PX
colnames(new)[c(2,4)] = c("SUB_GENE", "SUB_MOD_RSD")
new$log2FC = log2(abs(as.numeric(as.character(new$FC)))) # the as.numeric(as.character()) fixes an issue with the FC values as factors
new = new[complete.cases(new$log2FC),]
}
else {
double = PX[grep(";",PX$Residue.Both),]
residues = as.character(double$Residue.Both)
residues = as.matrix(residues, ncol = 1)
split = strsplit(residues, split = ";")
x = sapply(split, length)
single = data.frame(Protein = rep(double$Protein, x),
Gene = rep(double$Gene, x),
Peptide = rep(double$Peptide, x),
Residue.Both = unlist(split),
p = rep(double$p, x),
FC = rep(double$FC, x))
# create new object of PX that has all residues in separate rows
new = PX[-grep(";", PX$Residue.Both),]
new = rbind(new, single)
colnames(new)[c(2,4)] = c("SUB_GENE", "SUB_MOD_RSD")
new$log2FC = log2(abs(as.numeric(as.character(new$FC)))) # the as.numeric(as.character()) fixes an issue with the FC values as factors
new = new[complete.cases(new$log2FC),]
}
#----------------
# Process KSData dataset based on user input (NetworKIN=T/F and NetworKIN cutoff score)
if (NetworKIN == TRUE){
KSData.filtered = KSData[grep("[a-z]", KSData$Source),]
KSData.filtered = KSData.filtered[(KSData.filtered$networkin_score >= NetworKIN.cutoff),]
}
else{
KSData.filtered = KSData[grep("PhosphoSitePlus", KSData$Source),]
}
#----------------
# Extract KSData.filtered annotations that are only found in new
KSData.dataset = merge(KSData.filtered, new)
KSData.dataset = KSData.dataset[order(KSData.dataset$GENE),]
KSData.dataset$Uniprot.noIsoform = sapply(KSData.dataset$KIN_ACC_ID, function(x) unlist(strsplit(as.character(x), split="-"))[1])
# last expression collapses isoforms of the same protein for easy processing
KSData.dataset.abbrev = KSData.dataset[,c(5,1,2,16:19,14)]
colnames(KSData.dataset.abbrev) = c("Kinase.Gene", "Substrate.Gene", "Substrate.Mod", "Peptide", "p", "FC", "log2FC", "Source")
KSData.dataset.abbrev = KSData.dataset.abbrev[order(KSData.dataset.abbrev$Kinase.Gene, KSData.dataset.abbrev$Substrate.Gene, KSData.dataset.abbrev$Substrate.Mod, KSData.dataset.abbrev$p),]
# take the mean of the log2FC amongst phosphosite duplicates
KSData.dataset.abbrev = aggregate(log2FC ~ Kinase.Gene+Substrate.Gene+Substrate.Mod+Source, data=KSData.dataset.abbrev, FUN=mean)
KSData.dataset.abbrev = KSData.dataset.abbrev[order(KSData.dataset.abbrev$Kinase.Gene),]
#@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@#
# Do analysis for KSEA
#@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@#
kinase.list = as.vector(KSData.dataset.abbrev$Kinase.Gene)
kinase.list = as.matrix(table(kinase.list))
Mean.FC = aggregate(log2FC ~ Kinase.Gene, data=KSData.dataset.abbrev, FUN=mean)
Mean.FC = Mean.FC[order(Mean.FC[,1]),]
Mean.FC$mS = Mean.FC[,2]
Mean.FC$Enrichment = Mean.FC$mS/abs(mean(new$log2FC, na.rm=T))
Mean.FC$m = kinase.list
Mean.FC$z.score = ((Mean.FC$mS- mean(new$log2FC, na.rm=T))*sqrt(Mean.FC$m))/sd(new$log2FC, na.rm=T)
Mean.FC$p.value = pnorm(-abs(Mean.FC$z.score)) # 1-tailed p-value
Mean.FC$FDR = p.adjust(Mean.FC$p.value, method="fdr")
Mean.FC = Mean.FC[order(Mean.FC$Kinase.Gene), -2]
return(Mean.FC)
}
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