read.rflp: Read RFLP data

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/read.rflp.R

Description

Function to read RFLP data (e.g. generated with software package Gene Profiler 4.05 (Scanalytics Inc.)) for DNA fragment analysis and genotyping, and exported to a text file.

Usage

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Arguments

file

character: RFLP file to read in.

Details

The function reads data from a text file which was generated e.g. with the software package Gene Profiler 4.05 (Scanalytics Inc.) for DNA fragment analysis and genotyping. The data file contains sample identifier (Sample), band number (Band), molecular weight (MW) and gel identifier (Gel) (see RFLPdata).

If gel identifier Gel is missing it is extracted from the sample identifier Sample.

Value

A data.frame with variables

Sample

character: sample identifier.

Band

integer: band number.

MW

integer: molecular weight.

Gel

character: gel identifier.

Author(s)

Fabienne Flessa Fabienne.Flessa@uni-bayreuth.de,
Alexandra Kehl Alexandra.Kehl@uni-tuebingen.de,
Matthias Kohl Matthias.Kohl@stamats.de

References

Flessa, F., Kehl, A., Kohl, M. Analysing diversity and community structures using PCR-RFLP: a new software application. Molecular Ecology Resources 2013 Jul; 13(4):726-33.

See Also

RFLPdata, RFLPdist

Examples

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Dir <- system.file("extdata", package = "RFLPtools") # input directory 
filename <- file.path(Dir, "RFLPexample.txt")
RFLP1 <- read.rflp(file = filename)
str(RFLP1)

filename <- file.path(Dir, "AZ091016_report.txt")
RFLP2 <- read.rflp(file = filename)
str(RFLP2)

RFLPtools documentation built on May 4, 2021, 1:06 a.m.