getDataValuesDownload: Retrieve the values for a particular patients dataset

In SRHilz/GliomaAtlas3D: A 3D Map of Tumor-Wide Genetic and Microenvironmental Heterogeneity Present Across Adult Diffuse Glioma

Description

Creates a vector of final data values for a particular patient, tumor, and dataset

Usage

getDataValuesDownload(
  patientsFinal,
  sfConversion,
  datasetD,
  typeD,
  rowSelectionD,
  thresholdD,
  conversion,
  tumorDatasetsPath,
  sampleData
)

Arguments

patientsFinal	Patient ID in long form (i.e. Patient300 not P300)
sfConversion	Coverts patientID to sf# in a one-to-one relationship
datasetD	name of dataset (i.e. Histology, Amplification, Copy Number, etc)
typeD	only required if dataset is Histology
rowSelectionD	only required if dataset is Copy Number, RNAseq, Cell Types, Cancer-associated Processes, or Expansions
thresholdD	only required if dataset is Amplification
conversion	converts dataset to name of data file, where value is dataset and name is file name (ex c(cn.rds='Copy Number', ))
tumorDatasetsPath	path to datasets
sampleData	contains spatial information about each sample

SRHilz/GliomaAtlas3D documentation built on Nov. 25, 2020, 8:31 p.m.