exampleYAPSA: Test and example data

In YAPSA: Yet Another Package for Signature Analysis

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 [e-mail]

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)

YAPSA documentation built on Nov. 8, 2020, 4:59 p.m.