PTM-SEA Input Matrices
PTMSEA_INPUT.RdPhosphoproteomics differential-analysis results formatted as the input to PTM-SEA: one row per confidently localized phosphosite, one column per acute-exercise contrast, values are the differential-analysis z-statistics. This is an input file, not an enrichment result. PTM-SEA itself is run from the Broad Institute PTM-SEA / ssGSEA2.0 container against PTMsigDB, which is outside this package.
Sites are restricted to those flagged confident_site in the prot-ph
feature metadata (see ADIPOSE_PROT_PH_QC, MUSCLE_PROT_PH_QC). Contrasts
are contrast_type == "exercise_with_controls" with contrast_category in
"EE-CON" or "RE-CON". Muscle carries three post-exercise timepoints
crossed with the two exercise modalities; adipose was sampled at
post_3.5_4_hr only.
Each element is a GCT object, the S4 class defined by the cmapR
package. cmapR is in Suggests, not Imports: the object loads without it
and its slots are reachable as @mat, @rdesc, @cdesc, @rid and
@cid, but anything that dispatches on the class — printing the object,
the cmapR accessors, write_gct() — needs cmapR installed, as does
R CMD check to inspect the data.
Format
A named list of two cmapR GCT objects, "muscle" (16,469 sites x
6 contrasts) and "adipose" (7,287 sites x 2 contrasts). The mat slot
holds the z-statistics. The rdesc slot holds the prot-ph feature
annotation and the per-contrast logFC, p_value and adj_p_value.