read.abi {TRAMPR}

Read ABI Output Files

Description

Read an Applied Biosystems Gene Mapper (ABI) output file, and prepare for analysis.

Note that this operates on the summarised output (a text file), rather than the .fsa files containing data for individual runs.

Usage

read.abi(file)

Arguments

file

The name of the file from which the data are to be read.

Details

The ABI file format contains a few features that make it difficult to interact with directly, so read.abi provides a wrapper around read.table to work around these. The three issues are (1) trailing tab characters, (2) mixed case and punctuation in column names, and (3) parsing the “Dye/Sample Peak” column.

Because each line of an ABI file contains a trailing tab character (\t), read.table fails to read the file correctly. read.abi renames all columns so that non-alphanumeric characters all become periods, and all uppercase letters are converted to lower case.

The column Dye/Sample Peak contains data of the form <Dye>,<Sample Peak>, where <Dye> is a code for the dye colour used and <Sample Peak> is an integer indicating the order of the peaks. Entries where the contents of Dye/Sample Peak terminates in a "*" character (indicating an internal size standard) are automatically excluded from the analysis.

The final column names are:

• sample.file.name: Name of the file containing data.

• size: Size of the peak (in base pairs).

• height: Height of the peak (arbitrary units).

• dye: Code for dye used.

• sample.peak: Rank of peak within current sample.

In addition, other column names may be retained from ABI output, but not used.

Note

There is no reason that data from other types of output files could not be manually imported using TRAMPsamples. We welcome contributions for other major data formats.

See Also

load.abi, which attempts to construct a TRAMPsamples object from an ABI file (with a bit of user intervention).