exampleYAPSA {YAPSA} | R Documentation |
Data structures used in examples, tests and the 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
.
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)
Daniel Huebschmann huebschmann.daniel@googlemail.com
http://www.ncbi.nlm.nih.gov/pubmed/23945592
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)