metacoder (version 0.1.3)

primersearch: Use EMBOSS primersearch for in silico PCR

Description

A pair of primers are aligned against a set of sequences. The location of the best hits, quality of match, and predicted amplicons are returned. Requires the EMBOSS tool kit (http://emboss.sourceforge.net/) to be installed.

Usage

primersearch(input, forward, reverse, mismatch = 5, ...)
# S3 method for character
primersearch(input, forward, reverse, mismatch = 5, ...)
# S3 method for taxmap
primersearch(input, forward, reverse, mismatch = 5,
  sequence_col = "sequence", result_cols = NULL, ...)

Arguments

input

(character)

forward

(character of length 1) The forward primer sequence

reverse

(character of length 1) The reverse primer sequence

mismatch

An integer vector of length 1. The percentage of mismatches allowed.

...

Unused.

sequence_col

(character of length 1) The name of the column in obs_data that has the input sequences.

result_cols

(character) The names of columns to include in the output. By default, all output columns are included.

Value

An object of type taxmap

Installing EMBOSS

The command-line tool "primersearch" from the EMBOSS tool kit is needed to use this function. How you install EMBOSS will depend on your operating system:

Linux:

Open up a terminal and type:

sudo apt-get install emboss

Mac OSX:

The easiest way to install EMBOSS on OSX is to use homebrew. After installing homebrew, open up a terminal and type:

brew install homebrew/science/emboss

NOTE: This has not been tested by us yet.

Windows:

There is an installer for Windows here:

ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.5.0.0-setup.exe

NOTE: This has not been tested by us yet.

Examples

# NOT RUN {
result <- primersearch(rdp_ex_data, 
                       forward = c("U519F" = "CAGYMGCCRCGGKAAHACC"),
                       reverse = c("Arch806R" = "GGACTACNSGGGTMTCTAAT"),
                       mismatch = 10)
                       
heat_tree(result, 
          node_size = n_obs,
          node_label = name,
          node_color = prop_amplified,
          node_color_range = c("red", "yellow", "green"),
          node_color_trans = "linear",
          node_color_interval = c(0, 1),
          layout = "fruchterman-reingold")
# }
# NOT RUN {
# }