new.mave.filter: New MaveDB Filter Object
In jweile/rapimave: R API for MaveDB

Description Usage Arguments Details Value Examples

Constructor that creates a MaveDB filter object

1	new.mave.filter(data, verbose = TRUE)

`data`	A data.frame containing a MaveDB data set containing at least the two columns "hgvs" and "score".
`verbose`	Logical. If TRUE, prints status messages while loading data.

The resulting object offers a number of filter functions. All these functions return vectors of type logical, which can be combined with & and | to form more complex filters before being applied to the data. (See example below). The following functions are available.

mutationCount() filters by number of mutations in the variant. Parameters min and max default to 0 and Inf respectively.
position() filters by the (start) position of the mutations. Parameters min and max default to -Inf and Inf respectively. Parameter multi determines whether in case of multi-mutants, the criterium must match any or all of the individual mutations. Allowed values are "any" and "all".
residues() filters by amino acid residues. Parameter from and to are vectors of allowed ancestral and variant amino acid residues.Parameter multi determines whether in case of multi-mutants, the criterium must match any or all of the individual mutations. Allowed values are "any" and "all".
numerical() filters by numerical columns. Parameter col is the name of the numerical column to filter by. Parameters min and max default to -Inf and Inf respectively.
categorical() filters by categorical columns. Parameter col is the name of the categorical column (of type character or factor) to filter by. Parameter values is a vector of allowed values in that column to filter for.

a new MaveDB filter object

## Not run: 
mave <- new.rapimave()
data <- mave$getScores("SCS000001A.2")
mfilter <- new.mave.filter(data)
filter <- with(mfilter,
   position(min=5,multi="all") & residues(to="Ala",multi="all") & numerical("score",min=0.1)
)
filtered.data <- data[filter,]

## End(Not run)