inSilicoFragmentation: In silico fragmentation

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).

Value

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

Details

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

Examples

Run this code

inSilicoFragmentation("GGGTTAGTCC")