prepare_tcga_for_spongEffects: prepare TCGA formats for spongEffects

In mlist/SPONGE: Sparse Partial Correlations On Gene Expression

prepare TCGA formats for spongEffects

Description

prepare TCGA formats for spongEffects

Usage

prepare_tcga_for_spongEffects(
  tcga_cancer_symbol,
  normal_ceRNA_expression_data,
  tumor_ceRNA_expression_data,
  normal_metadata,
  tumor_metadata,
  clinical_data,
  tumor_stages_of_interest,
  subtypes_of_interest
)

Arguments

tcga_cancer_symbol	e.g., BRCA for breast cancer
normal_ceRNA_expression_data	normal ceRNA expression data (same structure as input for SPONGE)
tumor_ceRNA_expression_data	tumor ceRNA expression data (same structure as input for SPONGE)
normal_metadata	metadata for normal samples (TCGA format style, needs to include column: sampleID, PATIENT_ID)
tumor_metadata	metadata for tumor samples (TCGA format style, needs to include column: sampleID, PATIENT_ID)
clinical_data	clinical data for all patients (TCGA format style, needs to include column: PATIENT_ID, AJCC_PATHOLOGIC_TUMOR_STAGE)
tumor_stages_of_interest	array e.g., c(STAGE I', 'STAGE IA', 'STAGE IB', 'STAGE II', 'STAGE IIA')
subtypes_of_interest	array e.g., c("LumA", "LumB", "Her2", "Basal", "Normal")

Value

list of prepared data. You can access it with list$objectname for further spongEffects steps

mlist/SPONGE documentation built on Feb. 12, 2023, 1:22 a.m.