These functions help convert data from Applied Biosystems
Gene Mapper (ABI) output format into TRAMPsamples
objects for analysis. Note that this operates on the summarised
output (a text file), rather than the .fsa files containing
data for individual runs.
Details of the procedure of this function are given below, and a
worked example is given in the package vignette; type
vignette("TRAMPRdemo") to view it.
The function peakscanner.to.genemapper is an experimental
function to convert from peakscanner output to abi genemapper output.
The peakscanner output is very slightly different in format, and
currently load.abi is very fussy about the input file's
structure. Eventially load.abi will be made more tolerant, but
as an interim solution, run peakscanner.to.genemapper on your
file. By default, running
peakscanner.to.genemapper(myfile.csv) will produce a file
myfile.txt. This can then be loaded using load.abi as
described below, specifying myfile.txt as the file
argument.
load.abi(file, file.template, file.info, primer.translate, ...)
load.abi.create.template(file, file.template)
load.abi.create.info(file, file.template, file.info)peakscanner.to.genemapper(filename, output)
The name of the file from which the ABI data are to be read from.
The name of the file containing the “template” file (see Details).
(Optional) the name of the file containing extra information associated with each sample (see Details).
List used to translate dye codes into primers. The same codes are assumed to apply across the whole file. See Details for format.
Additional objects to incorportate
into a TRAMPsamples object. See TRAMPsamples
for details.
In peakscanner.to.genemapper, the name of the
csv file containing output.
In peakscanner.to.genemapper, the name of the
file to be output in abi format (if omitted, this will be
automatically generated).
Do not change the names of any columns produced by
load.abi.create.template or load.abi.create.info.
Some terminology: a “sample” refers to a physical sample
(e.g. a root tip), while a “run” refers to an individual
TRFLP run (i.e. one enzyme and one primer). Because two primers are
run at once, each “runfile” contains information on two
“runs”, but each “sample” may contain more than one
“runfile”. Runfiles are distinguished by different
sample.file.name values in the ABI file, while different
samples are distinguished by different
sample.fk/sample.pk values.
primer.translate is a list used to translate between the dyes
recorded in the ABI file and the primers used. Each element
corresponds to a different primer, and is a vector of different colour
dyes. The list:
list(ITS1F="B", ITS4="G")
would translate all dyes with the value "B" to "ITS1F",
and all dyes with the value "G" to "ITS4". The list:
list(ITS1F="B", ITS4=c("G", "Y"))
would do the same, except that both "G" and "Y"
dyes would be converted to "ITS4". If a dye is used in the
data that is not represented within primer.translate, then it
will be excluded (e.g., all rows of data with dye as
"R" will be excluded).
The procedure for loading in ABI data is:
Create the “template” file. Template files are
required to record which enzymes were used for each run, since that
is not included in the ABI output, and to group together separate
runs (typically different enzymes) that apply to the same
individual. The function load.abi.create.template will
create a template that contains all the unique file names found in
the ABI file (as sample.file.name), and blank columns titled
enzyme and sample.index. Running
load.abi.create.template(x)
where x is the name of your ABI file will create a template
file in the same directory as the ABI file. The function will print
the name and location of the template file to the console.
Edit the template file and save. The enzyme and
sample.index columns are initially empty and need filling in,
which can be done in Excel, or another spreadsheet program. The
sample.index column links sample.file.name back to an
individual sample; multiple sample.file.names that share
sample.index values come from the same individual sample.
(If editing with Excel, ignore all the warnings about incompatible
file formats when saving.) sample.index should be a positive
integer (but see Note below).
Optionally create an “info” file, which is useful if
you want to associate extra information against your samples. The
function load.abi.create.info will create an info file that
contains all the unique values of sample.index, and an empty
column titled species. The species column can be
filled in where the species is known (e.g. from collections of
sporocarps). Any additional columns may be added. Running
load.abi.create.info(x)
where x is the name of your ABI file will create an info
file in the same directory as the ABI file. The function will print
the name and location of the info file to the console. Edit and
save this file.
Create the TRAMPsamples object by running
load.abi. This loads your ABI data, plus the new template
file, plus an optional information file. Running
my.samples <- load.abi(x, primer.translate=primer.translate)
will create an object “my.samples” containing your
data.
By default, the filenames of the template and info files will be
automatically generated: <prefix>.<ext> becomes
<prefix>_template.csv or <prefix>_info.csv. If you
choose to specify file.template or file.info manually
when running load.info.create.template or
load.info.create.info, you must use the same values of
file.template and file.info when running
load.abi.
read.abi, which reads in ABI data with few
modifications.
TRAMPsamples, which documents the data type produced by
load.abi.
The package vignette, which includes a worked example of loading data
using these functions; to locate the vignette, type
help(library=TRAMPR), and scroll to the bottom of the page, or
type: system.file("doc/TRAMPR_demo.pdf", package="TRAMPR").