rnaDigest: RNA digest

In MassArray: Analytical Tools for MassArray Data

Description

Function to perform an in silico RNAse A digest for either the T or C cleavage reactions

Usage

rnaDigest(sequence, type = c("T", "C"))

Arguments

sequence	Nucleotide sequence input
type	One of either 'T' or 'C', specifying which cleavage reaction mixture was used

Value

Returns a list of MassArrayFragment objects, each containing information about a given fragment generated by the RNA digest

Author(s)

Reid F. Thompson ([e-mail]), John M. Greally ([e-mail])

See Also

See Also as MassArrayFragment

Examples

rnaDigest("AAAACCCCCTGCGGAGAGAGGCCGACAAAA", type="T")

Example output

[[1]]
An object of class "MassArrayFragment"
Slot "ID":
[1] 1

Slot "assay.name":
[1] ""

Slot "name":
[1] ""

Slot "sequence":
[1] "AAAACCCCCT"

Slot "position":
[1] 1

Slot "length":
[1] 10

Slot "CpGs":
[1] 0

Slot "MW":
[1] 3087.957

Slot "collisions":
[1] 0

Slot "collision.IDs":
list()

Slot "CG.collisions":
[1] 0

Slot "CG.collision.IDs":
list()

Slot "type":
[1] "T"

Slot "direction":
[1] "+"

Slot "extra":
[1] "5OH"

Slot "bisulfite.converted":
[1] TRUE

Slot "assayable":
[1] FALSE

Slot "conversion.control":
[1] FALSE

Slot "required":
[1] FALSE

Slot "ignored":
[1] FALSE

Slot "primer":
[1] FALSE


[[2]]
An object of class "MassArrayFragment"
Slot "ID":
[1] 2

Slot "assay.name":
[1] ""

Slot "name":
[1] ""

Slot "sequence":
[1] "GCGGAGAGAGGCCGACAAAA"

Slot "position":
[1] 11

Slot "length":
[1] 20

Slot "CpGs":
[1] 2

Slot "MW":
[1] 6571.115

Slot "collisions":
[1] 0

Slot "collision.IDs":
list()

Slot "CG.collisions":
[1] 0

Slot "CG.collision.IDs":
list()

Slot "type":
[1] "T"

Slot "direction":
[1] "+"

Slot "extra":
[1] "5OH"

Slot "bisulfite.converted":
[1] TRUE

Slot "assayable":
[1] FALSE

Slot "conversion.control":
[1] FALSE

Slot "required":
[1] FALSE

Slot "ignored":
[1] FALSE

Slot "primer":
[1] FALSE

MassArray documentation built on Nov. 8, 2020, 5:16 p.m.