inSilicoFragmentation: In silico fragmentation

In MassArray: Analytical Tools for MassArray Data

Description

Function to perform a complete in silico fragmentation of input sequence. Provides wrapper to a number of different functions, each of which determines additional information about each fragment.

Usage

inSilicoFragmentation(sequence, fwd.tag = "", rev.tag = "", type = c("T", "C"), lower.threshold = 1500, upper.threshold = 7000, fwd.primer = 0, rev.primer = 0, multiple.conversion = FALSE)

Arguments

sequence	Nucleotide sequence input as a character string
fwd.tag	Nucleotide tag sequence 5' of the forward primer
rev.tag	T7-containing nucleotide tag sequence 5' of the reverse primer
type	One of 'T' or 'C' indicating which cleavage reaction to use
lower.threshold	Lower limit (in Da) of usable mass window (default: 1500)
upper.threshold	Upper limit (in Da) of usable mass window (default: 7000)
fwd.primer	Length (in bp) of forward primer
rev.primer	Length (in bp) of reverse primer
multiple.conversion	Logical value specifying whether or not to include multiple CGs on the same conversion control fragment where possible (default is FALSE).

Details

In silico fragmentation analysis includes RNAse A digestion, peak mapping and overlap detection, CG detection, assayability and conversion controls.

Value

Returns a list of MassArrayFragment objects, each with extensive contextual and other information

Author(s)

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

See Also

See Also as MassArrayFragment

Examples

inSilicoFragmentation("GGGTTAGTCC")

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