R/datasets.R

In raerose01/deconstructSigs: Identifies Signatures Present in a Tumor Sample

#' Values for 100 randomly generated tumor samples
#' 
#' A dataset containing the value for the 96-trinucleotide contexts of 100 
#' tumors generated by a random linear combination of the Nature 2013
#' signatures.
#' 
#' @docType data
#' @keywords datasets
#' @name randomly.generated.tumors
#' @format A data frame of 100 rows and 96 columns
NULL

#' Published Signatures from Alexandrov et al 2013
#' 
#' A dataset containing the published signatures from Alexandrov et al read into
#' R as a data frame. Can be used the 'signatures.ref' parameter in
#' whichSignatures(). Data obtained: Nature 2013 PMID:23945592
#' 
#' @docType data
#' @keywords datasets
#' @name signatures.nature2013
#' @format A data frame of 27 rows and 96 columns
#' @source \url{http://www.ncbi.nlm.nih.gov/pubmed/23945592}
NULL

#' Published Signatures from Sanger COSMIC
#' 
#' A dataset containing the additional signatures identified read into R as a 
#' data frame. Can be used the 'signatures.ref' parameter in whichSignatures().
#' 
#' 
#' @docType data
#' @keywords datasets
#' @name signatures.cosmic
#' @format A data frame of 30 rows and 96 columns
#' @source \url{http://cancer.sanger.ac.uk/cosmic/signatures}
NULL

#' Updated SBS Exome Signatures from Sanger COSMIC (May 2019)
#' 
#' A dataset containing the additional signatures identified read into R as a 
#' data frame. Can be used the 'signatures.ref' parameter in whichSignatures().
#' 
#' 
#' @docType data
#' @keywords datasets
#' @name signatures.exome.cosmic.v3.may2019
#' @format A data frame of 65 rows and 96 columns
#' @source \url{https://www.synapse.org/#!Synapse:syn12009743}
NULL

#' Updated SBS Genome Signatures from Sanger COSMIC (May 2019)
#' 
#' A dataset containing the additional signatures identified read into R as a 
#' data frame. Can be used the 'signatures.ref' parameter in whichSignatures().
#' 
#' 
#' @docType data
#' @keywords datasets
#' @name signatures.genome.cosmic.v3.may2019
#' @format A data frame of 67 rows and 96 columns
#' @source \url{https://www.synapse.org/#!Synapse:syn12009743}
NULL

#' New DBS Signatures from Sanger COSMIC (May 2019)
#' 
#' A dataset containing the double base substitution signatures identified read into R as a 
#' data frame. Can be used the 'signatures.ref' parameter in whichSignatures().
#' 
#' 
#' @docType data
#' @keywords datasets
#' @name signatures.dbs.cosmic.v3.may2019
#' @format A data frame of 11 rows and 78 columns
#' @source \url{https://www.synapse.org/#!Synapse:syn12009743}
NULL

#' Table of Possible DBS mutations and their reverse complement
#' 
#' A dataset containing the additional signatures identified read into R as a 
#' data frame. Can be used the 'signatures.ref' parameter in whichSignatures().
#' 
#' 
#' @docType data
#' @keywords datasets
#' @name dbs_possible
#' @format A data frame of 30 rows and 96 columns
#' @source \url{https://www.synapse.org/#!Synapse:syn12009743}
NULL

#' The counts of every trinuclotide frequency in an exome
#' 
#' A datset containing the number of times each trinucleotide (ex: ACA) is found
#' in the exome region captured by sequencing. Can be used as the
#' 'trimer.counts.loc' parameter in whichSignatures().
#' 
#' @docType data
#' @keywords datasets
#' @name tri.counts.exome
#' @format A data frame of 32 rows and 1 column that contains the counts
NULL

#' The counts of every trinuclotide frequency in a genome
#' 
#' A datset containing the number of times each trinucleotide (ex: ACA) is found
#' in the hg19 genome. Can be used as the
#' 'trimer.counts.loc' parameter in whichSignatures().
#' 
#' @docType data
#' @keywords datasets
#' @name tri.counts.genome
#' @format A data frame of 32 rows and 1 column that contains the counts
NULL

#' Example output of whichSignatures()
#' 
#' A list that was generated from running whichSignatures().  It contains the
#' following:
#' 
#' \itemize{ \item weights - weight of each signature found in the sample \item
#' tumor - tricontext fractions that were used as input \item product - product
#' of the weights by the reference signatures used \item diff - difference
#' between the tumor tricontexts fractions used as input and those generated as
#' the product \item unknown - the fraction of the tumor profile that could not
#' be assigned to a signature }
#' 
#' @docType data
#' @keywords datasets
#' @name example.output
#' @format A list of four elements
NULL

#'Example input to mut.to.sigs.input()
#'
#'A data frame containing example mutations that can be used as input to 
#'mut.to.sigs.input(). Data comes from two TCGA LUAD patients 
#'(http://cancergenome.nih.gov/) Contains the following columns:
#'
#'\itemize{ \item Sample - sample name \item chr - chromosome number \item pos -
#'chromosome position \item ref - reference base \item alt - alternate base }
#'
#' @docType data
#' @keywords datasets
#' @name sample.mut.ref
#' @format A data frame of 657 rows and 5 column that contains example mutations 
#'  which could be used in mut.to.sigs.input()
#' @source \url{http://cancergenome.nih.gov/}
NULL