sigSim: Get the similarity score of a tumor sample with mSignaturedb

In 13thirteen-w/Rpackage_cpSig: Compute 30 signatures similarity between reference and tumor sample

Description

Get the similarity score of a tumor sample with mSignaturedb

Usage

sigSim(trTmMut, clinicalData, tmMutRef = mSigdb, contexts.needed = FALSE,
  tri.counts.method = "default")

Arguments

trTmMut	Either a data frame or location of input text file, where rows are samples, columns are trinucleotide contexts. Use data(sample.mut.trans) to see the example data.
clinicalData	Location of the mutation file that is to be converted or name of data frame in environment. Include country and site information of every sample in trTmMut. Use data("sample.clinical") to see the example data.
tmMutRef	Location of the mutation file that is to be converted or name of data frame in environment. "tmMutRef" is the standard signature value for one site and one country. Default value is "mSigdb" that convert from "mSignatureDB" database. USe data("mSigdb") to see the example dasta.
contexts.needed	FALSE if tumor.file is a context file, TRUE if it is only mutation counts.
tri.counts.method	Set to either: 'default' – no further normalization 'exome' – normalized by number of times each trinucleotide context is observed in the exome 'genome' – normalized by number of times each trinucleotide context is observed in the genome 'exome2genome' – multiplied by a ratio of that trinucleotide's occurence in the genome to the trinucleotide's occurence in the exome 'genome2exome' – multiplied by a ratio of that trinucleotide's occurence in the exome to the trinucleotide's occurence in the genome data frame containing user defined scaling factor – count data for each trinucleotide context is multiplied by the corresponding value given in the data frame

Value

The similarity score of a tumor sample with mSignaturedb

Examples

testSim = sigSim(trTmMut = sample.mut.trans, clinicalData = sample.clinical, contexts.needed = TRUE)

13thirteen-w/Rpackage_cpSig documentation built on May 8, 2019, 1:42 p.m.