ampliconPrediction {MassArray} | R Documentation |
Function to predict amplicon fragmentation pattern and details for T&C reactions on the plus and minus strands
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)
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 |
table |
Logical specifying whether or not to return tabular representation of fragmentation profiles (default is |
lwd |
The line width used for fragmentation display, a positive number, defaulting to |
cex |
A numerical value (defaulting to |
multiple.conversion |
Logical value specifying whether or not to include multiple CGs on the same conversion control fragment where possible (default is |
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.
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 |
Reid F. Thompson (rthompso@aecom.yu.edu), John M. Greally (jgreally@aecom.yu.edu)
ampliconPrediction("TGGAACACCCAGCAAAGATCAAGCAGGAAAGGGCGCACGCAGCCTTCGTTGCTAACCTCCTCTGGACTCTGGTACCCCAGGCACCGCGAATGCTCCCCACCTCAGCCCCCTGACCTTTACCATCGCTGAAGCGGGCGTCGCTGATGTCTGCGGCGAGCCTGCCGACCAGCCCAGCTGCCCAGAGGAGCAGCCAGGCAAGGGCGCTGGCAGCCAGGACGCCGGAGCCCGACGCCCGAGAGGGGCGCGCGGAGCAAGCTGCGGTCACGGGAGGAACCTGAGCACGCAGAGCGTACCCCCACCTTCCACGGTGACCCGGACAGAACGCTCCTTGCGCTCCCACCCTAGGACCCCCTGTAACTCCAGGTTCCTGAGA")