icgc2mut: Converts an ICGC file into a mutation file
In antoine186/convSig: Mutational Process Inference via Expectation Maximisation

Description Usage Arguments Value Details Examples

Converts an ICGC file into a mutation file

1	icgc2mut(datapath, assembly = NULL, Seq = NULL, using.vcf = FALSE)

`datapath`	The path leading to your ICGC file (tsv or csv only). Alternatively, this is your mutation data if you supplied either a `data.frame` or a `matrix`. Please make sure that your input data is not malformed; See loadICGCexample() for an example of an acceptable input.
`assembly`	This indicates the assembly version used in your experiment. Default is set to `NULL`.
`Seq`	A string or a variable referencing a string. This indicates the sequencing strategy/approach used in your genome experiment. Default is set to `NULL`.

A mutation file containing 6 fields: The ICGC sample ID, the chromosome ID, the chromosome start position, the chromosome end position, the reference allele, and the alternate allele.

Your input ICGC file must have a header abiding to the ICGC format. The presence of column headers 'mutated_from_allele' and 'mutated_to_allele' are absolute requirements for the usage of this function. You can also technically omit 'assembly_version' and 'sequencing_strategy' if you do not pass them as arguments. However, if you do, then they become requirements. The 'chromosome' header can also be omitted; This is not recommended however as the function will process mutations in the X and Y chromosomes instead of skipping them if they are present in the input file. See loadICGCexample() for a closer look at a legal input format.

res <- icgc2mut("simple_somatic_mutation.open.COCA-CN.tsv")
# Or
datapath <- "simple_somatic_mutation.open.COCA-CN.tsv"
res <- icgc2mut(datapath, "GRCh37", "WGS")