A parameter class for representing all parameters needed for running
the bsapply method.
Objects from the Class
Objects can be created by calls of the form new("BSParams", ...).
Slots
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.
Methods
bsapply(p)
Performs the function FUN using the
parameters contained within BSParams.