The Conventional PAM50 Approach
For comparison with PAM50 cases, we provide the function makeCalls.ihc to produce conventional PAM50 intrinsic subtype calls. Please note that the setup (loading the test data) is the same as Step 1 of the PCAPAM50 approach.
1) Call the Function:
Call the function makeCalls.ihc() on test data. Refer to the manual for detailed documentation on usage and arguments.
inputDir <- "Calls.PAM50"
res.PAM50 <- makeCalls.ihc(df.cln = df.cln, seed = 118, mat = Test.matrix, inputDir = inputDir)
The function returns a list containing:
- Int.sbs - Data frame with integrated subtype and clinical data. - score.fl - Data frame with scores from subtype predictions. - mdns.fl - Data frame with median values for each gene in the ER-balanced set. - SBS.colr - Colors associated with each subtype from the prediction results. - outList - Detailed results from subtype prediction functions.
A heatmap is generated within the inputDir folder.
Ihc.Mdns_PAM50_normalized_heatmap.pdf