exampleYAPSA {YAPSA} | R Documentation

## Test and example data

### Description

Data structures used in examples, SNV tests and the SNV signature vignette of the YAPSA package.

`lymphoma_PID_df`: A data frame carrying subgroup information for a subcohort of samples used in the vignette. Data in the vignette is downloaded from ftp://ftp.sanger.ac.uk/pub/cancer/AlexandrovEtAl/somatic_mutation_data/Lymphoma B-cell/Lymphoma B-cell_clean_somatic_mutations_for_signature_analysis.txt. In the file available under that link somatic point mutation calls from several samples are listed in a vcf-like format. One column encodes the sample the variant was found in. In the vignette we want to restrict the analysis to only a fraction of these involved samples. The data frame `lymphoma_PID_df` carries the sample identifiers (PID) as rownames and the attributed subgroup in a column called `subgroup`.

`lymphoma_test_df`: A data frame carrying point mutation calls. It represents a subset of the data stored in ftp://ftp.sanger.ac.uk/pub/cancer/AlexandrovEtAl/somatic_mutation_data/Lymphoma B-cell/Lymphoma B-cell_clean_somatic_mutations_for_signature_analysis.txt. In the file available under that link somatic point mutation calls from several samples are listed in a vcf-like format. One column encodes the sample the variant was found in. The data frame `lymphoma_test_df` has only the variants occuring in the sample identifiers (PIDs) 4112512, 4194218 and 4121361.

`lymphoma_Nature2013_raw_df`: A data frame carrying point mutation calls. It represents a subset of the data stored in ftp://ftp.sanger.ac.uk/pub/cancer/AlexandrovEtAl/somatic_mutation_data/Lymphoma B-cell/Lymphoma B-cell_clean_somatic_mutations_for_signature_analysis.txt. In the file available under that link somatic point mutation calls from several samples are listed in a vcf-like format. One column encodes the sample the variant was found in.

`lymphoma_Nature2013_COSMIC_cutoff_exposures_df`: Data frame with exposures for testing the plot functions. Data taken from ftp://ftp.sanger.ac.uk/pub/cancer/AlexandrovEtAl/somatic_mutation_data/Lymphoma B-cell/Lymphoma B-cell_clean_somatic_mutations_for_signature_analysis.txt.

`rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df`: Data frame with normalized or relative exposures for testing the plot functions. Data taken from ftp://ftp.sanger.ac.uk/pub/cancer/AlexandrovEtAl/somatic_mutation_data/Lymphoma B-cell/Lymphoma B-cell_clean_somatic_mutations_for_signature_analysis.txt.

`COSMIC_subgroups_df`: Subgroup information for the data stored in `lymphoma_Nature2013_COSMIC_cutoff_exposures_df` and `rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df`.

`chosen_AlexInitialArtif_sigInd_df`: Signature information for the data stored in `lymphoma_Nature2013_COSMIC_cutoff_exposures_df` and `rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df`.

`chosen_signatures_indices_df`: Signature information for the data stored in `lymphoma_Nature2013_COSMIC_cutoff_exposures_df` and `rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df`.

### Usage

    data(lymphoma_PID)

    data(lymphoma_test)

    data(lymphoma_Nature2013_raw)

    data(lymphoma_cohort_LCD_results)

    data(lymphoma_cohort_LCD_results)

    data(lymphoma_cohort_LCD_results)

    data(lymphoma_cohort_LCD_results)

    data(lymphoma_cohort_LCD_results)

### Author(s)

Daniel Huebschmann huebschmann.daniel@googlemail.com

### References

http://www.ncbi.nlm.nih.gov/pubmed/23945592

### Examples

    data(lymphoma_test)
    head(lymphoma_test_df)
    dim(lymphoma_test_df)
    table(lymphoma_test_df$PID)

    data(lymphoma_Nature2013_raw)
    head(lymphoma_Nature2013_raw_df)
    dim(lymphoma_Nature2013_raw_df)

[Package YAPSA version 1.16.0 Index]