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Last data update: 2014.03.03

R: Amplicon prediction

ampliconPrediction

R Documentation

Amplicon prediction

Description

Function to predict amplicon fragmentation pattern and details for T&C reactions on the plus and minus strands

Usage

ampliconPrediction(sequence, lower.threshold = 1500, upper.threshold = 7000, fwd.tag = "AGGAAGAGAG", rev.tag = "AGCCTTCTCCC", plot = TRUE, table = TRUE, lwd = 1, cex = 1, multiple.conversion = FALSE)

Arguments

`sequence`	Nucleotide sequence input as a character string
`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.tag`	Nucleotide tag sequence 5' of the forward primer
`rev.tag`	T7-containing nucleotide tag sequence 5' of the reverse primer
`plot`	Logical specifying whether or not to display graphical representation of fragmentation profiles (default is `TRUE`)
`table`	Logical specifying whether or not to return tabular representation of fragmentation profiles (default is `TRUE`)
`lwd`	The line width used for fragmentation display, a positive number, defaulting to `1`
`cex`	A numerical value (defaulting to `1`) giving the amount by which plotting text and symbols should be magnified relative to the default
`multiple.conversion`	Logical value specifying whether or not to include multiple CGs on the same conversion control fragment where possible (default is `FALSE`).

Details

Plotted fragmentation patterns contain a number of detailed features including: CG positions, molecular weight overlaps, conversion controls, fragment assayability, and more.

Note that the graphical output does not contain a built-in legend at this time, but the plot may be interepreted as follows: Putative fragmentation patterns are shown for T and C-cleavage reactions on both the plus and minus strands of an input amplicon, with the T-forward, T-reverse, C-forward, and C-reverse shown in descending order. CG dinucleotides (filled circles) are numbered and colored in blue. Other fragments are colored according to their ability to be assayed: fragment molecular weight outside the testable mass window (gray), fragment molecular weight overlapping with another fragment (red), fragment containing a potential conversion control (green), or fragment uniquely assayable but containing no CGs (black). Linked arrowheads denote molecular weight overlaps between multiple CG-containing fragments. Yellow highlights represent tagged or primer sequences, while lavender highlights denote user-specified "required" sites.

Value

If table is TRUE, returns a list containing the following items:

`summary`	A summary matrix of logical values specifying whether or not each CG is assayable by a given combination of cleavage reaction and DNA strand
`counts`	A numerical tally of the quantity of CGs that are assayable by each assay

Author(s)

Reid F. Thompson (rthompso@aecom.yu.edu), John M. Greally (jgreally@aecom.yu.edu)

Examples

ampliconPrediction("TGGAACACCCAGCAAAGATCAAGCAGGAAAGGGCGCACGCAGCCTTCGTTGCTAACCTCCTCTGGACTCTGGTACCCCAGGCACCGCGAATGCTCCCCACCTCAGCCCCCTGACCTTTACCATCGCTGAAGCGGGCGTCGCTGATGTCTGCGGCGAGCCTGCCGACCAGCCCAGCTGCCCAGAGGAGCAGCCAGGCAAGGGCGCTGGCAGCCAGGACGCCGGAGCCCGACGCCCGAGAGGGGCGCGCGGAGCAAGCTGCGGTCACGGGAGGAACCTGAGCACGCAGAGCGTACCCCCACCTTCCACGGTGACCCGGACAGAACGCTCCTTGCGCTCCCACCCTAGGACCCCCTGTAACTCCAGGTTCCTGAGA")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MassArray)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MassArray/ampliconPrediction.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ampliconPrediction
> ### Title: Amplicon prediction
> ### Aliases: ampliconPrediction
> ### Keywords: graphs attribute character aplot
> 
> ### ** Examples
> 
> ampliconPrediction("TGGAACACCCAGCAAAGATCAAGCAGGAAAGGGCGCACGCAGCCTTCGTTGCTAACCTCCTCTGGACTCTGGTACCCCAGGCACCGCGAATGCTCCCCACCTCAGCCCCCTGACCTTTACCATCGCTGAAGCGGGCGTCGCTGATGTCTGCGGCGAGCCTGCCGACCAGCCCAGCTGCCCAGAGGAGCAGCCAGGCAAGGGCGCTGGCAGCCAGGACGCCGGAGCCCGACGCCCGAGAGGGGCGCGCGGAGCAAGCTGCGGTCACGGGAGGAACCTGAGCACGCAGAGCGTACCCCCACCTTCCACGGTGACCCGGACAGAACGCTCCTTGCGCTCCCACCCTAGGACCCCCTGTAACTCCAGGTTCCTGAGA")
$summary
   required summary    T+    C+    T-    C-
1     FALSE    TRUE  TRUE FALSE FALSE FALSE
2     FALSE   FALSE FALSE FALSE FALSE FALSE
3     FALSE    TRUE  TRUE  TRUE FALSE  TRUE
4     FALSE    TRUE  TRUE  TRUE  TRUE FALSE
5     FALSE    TRUE  TRUE FALSE  TRUE  TRUE
6     FALSE    TRUE  TRUE  TRUE FALSE FALSE
7     FALSE    TRUE  TRUE FALSE  TRUE FALSE
8     FALSE    TRUE  TRUE FALSE  TRUE FALSE
9     FALSE    TRUE  TRUE FALSE FALSE FALSE
10    FALSE    TRUE  TRUE FALSE  TRUE FALSE
11    FALSE    TRUE  TRUE FALSE  TRUE FALSE
12    FALSE    TRUE  TRUE FALSE  TRUE FALSE
13    FALSE    TRUE  TRUE FALSE FALSE FALSE
14    FALSE    TRUE  TRUE FALSE FALSE FALSE
15    FALSE    TRUE  TRUE FALSE FALSE  TRUE
16    FALSE    TRUE  TRUE FALSE FALSE FALSE
17    FALSE    TRUE  TRUE FALSE FALSE FALSE
18    FALSE    TRUE  TRUE FALSE FALSE  TRUE
19    FALSE    TRUE  TRUE FALSE FALSE FALSE
20    FALSE    TRUE  TRUE FALSE FALSE FALSE
21    FALSE    TRUE  TRUE FALSE FALSE  TRUE
22    FALSE    TRUE  TRUE FALSE  TRUE FALSE
23    FALSE    TRUE  TRUE  TRUE  TRUE  TRUE
24    FALSE    TRUE FALSE FALSE  TRUE FALSE
25    FALSE    TRUE  TRUE FALSE  TRUE FALSE
26    FALSE    TRUE  TRUE  TRUE  TRUE  TRUE
27    FALSE    TRUE  TRUE  TRUE  TRUE FALSE
28    FALSE    TRUE  TRUE FALSE  TRUE FALSE
29    FALSE    TRUE  TRUE FALSE  TRUE FALSE

$counts
         summary  + T+ C+  - T- C-
all           28 27 27  6 19 15  7
required       0  0  0  0  0  0  0

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>