BreastOutput_TradScaled

BreastOutput_TradScaled.RData is an R-workspace contains the objects: allPs, allPs.adj, sumTable. These were generated from applying the SAPS method to the breast cancer meta-data set scaled by transforming each feature into its Z score across all patients in a data-set prior to merging across data-sets

sapsFigures

sapsFigures.R – This R script generates the figures, tables, and file used for clusterin

OvaryOutput_TradScaled

OvaryOutput_TradScaled.RData contains the objects: allPs, allPs.adj, sumTable.BreastOutput_TradScaled.RData. These were generated from applying the SAPS method to the ovarian cancer meta-data set scaled by transforming each feature into its Z score across all patients in a data-set prior to merging across data-sets

FinalOutput_Breast

FinalOutput_Breast.RData contains the results from the subtype-specific analysis in breast cancer, including the results of the permutation-based procedure to compute p values and q values for the SAPSscores

saps

saps.R – This R script provides R commands for loading data, applying the SAPS method, and generating the SAPS p values. The script is interactive, and the user must specify the working directory, and if the analysis is on the ovarian or breast data

BreastOutput_SubScaled

BreastOutput_SubScaled.RData is an R-workspace contains the objects: allPs, allPs.adj, sumTable. These were generated from applying the SAPS method to the breast cancer meta-data set scaled by transforming each feature into its Z score across all patients within a breast cancer subtype data-set prior to merging across data-sets

Breast_ERHigh_GSEA_Results

Results from GSEA Analysis in ER+ high proliferation subtype of breast cance

Breast_Her2_GSEA_Results

Results from GSEA Analysis in HER2+ subtype of breast cance

Ovary.Ps.OnPermutedData.RData

ReadMe, Ovary.Ps.OnPermutedData.RData. Ovary.Ps.OnPermutedData.RData contains the results of performing SAPS using permuted gene sets on the ovarian data. P_enrich, p_pure,p_randare arrays with P_enrich,P_pure, and P_random p values from permuted gene sets

Ovary_NonAngio_GSEA_Results

Results from GSEA Analysis in Non-Angiogenic subtype of ovarian cance