Description Usage Format Details Source Examples
Example mutation data
1 |
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
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.
Durinck, S, et al. (2011). “Temporal Dissection of Tumorigenesis in Primary Cancers." Cancer Discovery, 1(2), 137-143.
1 2 3 4 |
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
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