demoHLADataset: The HLA typing information from multiple samples stored in a...

In NCBI-Hackathons/Integrating-HLA-typing-methods-and-RNA-seq: HLA typing clustering and visualization based on specific similarity metrics

Description

This dataset can be used to test calculateHamming and TODO(AUTRE METRIC) functions.

Usage

data(demoHLADataset)

Format

a list of class HLADataset containing the following elements:

• data a tibble object containing the HLA typing information for all samples. The columns are:

  • SampleName a character string that represent the name of the sample.

  • AllelName a character string that represent the name of the allele (1 or 2).

  • GeneName a character string that represent the name of the HLA gene.

  • AlleleGroup a character string that represent the section identifying the subtype group.

  • Protein a character string that represent the section identifying the nucleotide substitutions group.

  • SynSubst a character string that represent the section identifying the synonymous nucleotide substitutions group.

  • NonCoding a character string that represent the section identifying the non-coding polymorphisms group.

  • Suffix a character string that represent the suffix of the HLA typing or NA.

Value

a list of class HLADataset containing the following elements:

• data a tibble object containing the HLA typing information for all samples. The columns are:

  • SampleName a character string that represent the name of the sample.

  • AllelName a character string that represent the name of the allele (1 or 2).

  • GeneName a character string that represent the name of the HLA gene.

  • AlleleGroup a character string that represent the section identifying the subtype group.

  • Protein a character string that represent the section identifying the nucleotide substitutions group.

  • SynSubst a character string that represent the section identifying the synonymous nucleotide substitutions group.

  • NonCoding a character string that represent the section identifying the non-coding polymorphisms group.

  • Suffix a character string that represent the suffix of the HLA typing or NA.

See Also

• calculateHamming for calculating the Hamming distance metric between all samples

Examples

## Load example dataset
data(demoHLADataset)

## Calculate Hamming distance metric
calculateHamming(demoHLADataset)

NCBI-Hackathons/Integrating-HLA-typing-methods-and-RNA-seq documentation built on Nov. 23, 2019, 1:57 a.m.