BSParams-class: Class "BSParams"

Description

A parameter class for representing all parameters needed for running the bsapply method.

Objects can be created by calls of the form new("BSParams", ...).

X:: a BSgenome object that contains chromosomes that you wish to apply FUN on
FUN:: the function to apply to each chromosome in the BSgenome object 'X'
exclude:: this is a character vector with strings that will be used to filter out chromosomes whose names match these strings.
simplify:: TRUE/FALSE value to indicate whether or not the function should try to simplify the output for you.
maskList:: A named logical vector of maskStates preferred when used with a BSGenome object. When using the bsapply function, the masks will be set to the states in this vector.
motifList:: A character vector which should contain motifs that the user wishes to mask from the sequence.
userMask:: A RangesList object, where each element masks the corresponding chromosome in X. This allows the user to conveniently apply masks besides those included in X.
invertUserMask:: A logical indicating whether to invert each mask in userMask.

bsapply(p): Performs the function FUN using the parameters contained within BSParams.