PhenoData: Dataset of sample annotation and phenotype information for 65...

In uclahs-cds/public-R-NanoStringNormCNV: Helper Functions to Normalize NanoString CNV Data

Dataset of sample annotation and phenotype information for 65 prostate cancer samples

Description

Sample annotation and phenotype information describing 65 NanoString prostate cancer samples. The same NanoString samples are found in the NanoString.DNA.raw dataset.

Usage

PhenoData

Format

A data-frame with 9 columns and 65 rows. Each row indicates a different NanoString DNA sample. The columns either annotate the sample or describe a feature of it:

SampleID

The sample ID is unique to each row (or NanoString sample).

Patient

The patient ID is specific to an individual patient that provided one or more tissue samples for the study.

Name

The sample name is unique to a tumour/normal tissue sample. Each tissue sample can have one or more replicates (also referred to as NanoString samples) which are distinguished by sample IDs ('SampleID').

Cartridge

The cartridge the NanoString sample was processed on. All numeric values.

Type

The sample type, either 'Tumour' or 'Reference' (also referred to as a normal).

ReferenceID

The sample ID of the sample's matched normal. This only applies to tumour samples so for reference samples this value is NA. For tumour samples with no matched normal, 'missing' is used.

HasReplicate

Whether the sample has replicates (1) or not (0).

Sex

The sex of the patient that provided the sample. The following notation is used: 'M' for male, 'F' for female, NA for unknown. Sample sex is required to perform CNA calling on sex chromosome probes.

Fragmentation

The DNA fragmentation used: sonication or AluI restriction site digestion. This column is optional. The information is only used when selecting samples for a quality check using restriction fragmentation controls.

Author(s)

Dorota Sendorek

Examples

	data(PhenoData);

uclahs-cds/public-R-NanoStringNormCNV documentation built on May 31, 2024, 9:09 p.m.