cancerTiming (version 3.1.8)

mutData: Example Mutation Data

Description

Example mutation data

Usage

data(mutData)

Format

A data frame with 1007 observations on the following 10 variables.

chromosome

chromosome

position

position

refbase

reference base at this location

mutbase

variant base at this location

rsID

dbSNP database number, NA if not in database.

t_ref_count

number of fragments in tumor with the reference base

t_alt_count

number of fragments in tumor with the variant base

allelefreq

observed allele frequency

n_ref_count

number of fragments in normal with the ref base

n_alt_count

number of fragments in normal with the variant base

Source

Durinck, S, et al. (2011). ``Temporal Dissection of Tumorigenesis in Primary Cancers." Cancer Discovery, 1(2), 137-143.

Details

Mutation data from chr17. The CNLOH region is from positions 0 to 1.8E7. The normal contamination estimate in the paper was given as 0.22.

Examples

data(mutData)
head(mutData)
#only mutations in the CNLOH region
onlyMuts<-subset(mutData,is.na(rsID) & position <= 1.8E7)