BSParams-class: Class "BSParams"

In BSgenome: Software infrastructure for efficient representation of full genomes and their SNPs

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 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.

Author(s)

Marc Carlson

See Also

bsapply

BSgenome documentation built on Nov. 8, 2020, 7:48 p.m.