mutData: Example Mutation Data

In cancerTiming: Estimation of Temporal Ordering of Cancer Abnormalities

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

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.

Source

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

Examples

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

Example output

  chromosome position refbase mutbase       rsID t_ref_count t_alt_count
1         17   263602       A       G rs71356791           1          29
2         17   263610       G       C rs35229416           9          14
3         17   263821       A       G  rs9891763           0          96
4         17   412525       G       A  rs2075443           0         181
5         17   632390       G       T rs11546732           0          34
6         17   917163       C       T  rs2262150          37           7
  allelefreq n_ref_count n_alt_count
1   0.966667           0          25
2   0.608696           1          17
3   1.000000           0          60
4   1.000000           1         123
5   1.000000           0          29
6   0.159091          15          37

cancerTiming documentation built on May 2, 2019, 9:28 a.m.