BSParams-class {BSgenome} | R Documentation |
Class "BSParams"
Description
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 treated as regular expressions 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 IntegerRangesList object, where each element masks the corresponding chromosome in
X
. This allows the user to conveniently apply masks besides those included inX
. invertUserMask
:-
A
logical
indicating whether to invert each mask inuserMask
.
Methods
bsapply(p)
Performs the function FUN using the parameters contained within
BSParams
.
Author(s)
Marc Carlson