| PX {KSEAapp} | R Documentation |
PX dataset for KSEA calculations
Description
A sample PX dataset of the experimental phosphoproteomics input
Usage
data(PX)
Format
the experimental data file must be formatted exactly as described below; must have 6 columns in the exact 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 the control sample is the denominator
References
unpublished data