Reads a dataframe of Peptides IDs and their Scores and run KEA3

reads a dataframe of Peptides IDs and their Scores (LFC, p-value, ... etc) and run KEA3 on a subset of these peptides or all of them

read_kea(
  df,
  filter = T,
  cutoff = 0.2,
  cutoff_abs = T,
  direction = "higher",
  rm_duplicates = T,
  method = "MeanRank",
  lib = c("kinase-substrate"),
  ...
)

Arguments

df	dataframe, must have at least Peptide and Score columns
filter	boolean to subset peptides or not
cutoff	numeric to act as the cutoff to filter out peptides
cutoff_abs	boolean (use absolute value or not) default is TRUE
direction	("lower", "higher) filter based on lower than or higher than the cutoff values (default to "higher")
rm_duplicates	boolean (TRUE or FALSE) remove genes duplicates
method	"MeanRank" takes the mean rank across all libraries or "MeanFDR" takes the mean of FDR across all libraries (default is "MeanRank")
lib	searched kea libraries "kinase-substrate" or "all" (default is "kinase-substrate" which will return only kinase libraries like ChengKSIN, PTMsigDB, PhosDAll)
...,	arguments passed to rank_kinases function

Value

dataframe, Ranked and quartiled table

Details

This function a dataframe of Peptides IDs and their Scores (LFC, p-value, ... etc) and run KEA3 on a subset of these peptides or all of them