BSgenome (version 1.40.1)

BSParams-class: Class "BSParams"

Description

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

Arguments

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.

See Also

bsapply