ICAMS: AddSeqContext – R documentation

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AddSeqContext

Add sequence context to a data frame with mutation records

Add sequence context to a data frame with mutation records

AddSeqContext(df, ref.genome, seq.context.width = 10, name.of.VCF = NULL)

`df`	An input data frame storing mutation records of a VCF file.
`ref.genome`	A `ref.genome` argument as described in `ICAMS`.
`seq.context.width`	The number of preceding and following bases to be extracted around the mutated position from `ref.genome`. The default value is 10.

A copy of the input data.frame with a new column added that contains sequence context information.

In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

v2.3.10

GPL-3 | file LICENSE

Authors

Steve Rozen, Nanhai Jiang, Arnoud Boot, Mo Liu, Yang Wu

Initial release