prepare_tcga_for_spongEffects: prepare TCGA formats for spongEffects

View source: R/fn_spongeffects_utility.R

prepare_tcga_for_spongEffectsR Documentation

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


biomedbigdata/SPONGE documentation built on Feb. 6, 2023, 10:19 p.m.