fastReadFrag: Reads tab delimited text files with input fragment sizes...

In kkeenan02/MsatAllele: Visualizes the scoring and binning of microsatellite fragment sizes

Description

Reads input text files with continuous fragment size data and creates an R data base.

Usage

fastReadFrag(in.file, date, plate, long = FALSE, keep.missing = FALSE)

Arguments

in.file	The name of the input file
date	A relevant date to be written on the data base
plate	A sample plate code to be written on the data base
long	Determines whether homozygotes should be stored as a single row or two.
keep.missing	retain missing data rows in the output dataframe

Details

This functions reads tab delimited files with the following fields: 1st column-sample name; 2nd column-Panel or test name (specific combination of loci in that sample); 3rd column-Locus name; 4th column-fragment size for first allele; 5th column-fragment size for 2nd allele. Use NA to code absent data.

Value

Marker	Genetic marker code
Sample	Sample code
Read	Fragment size
Date	Date
Plate	Plate code

Author(s)

Kevin Keenan

References

Alberto F. MsatAllele_1.0: an R package to visualize the binning of microsatellite alleles Journal of Heredity. 100(3):394,397

See Also

read.ah.file, AlleleCum, subdataBase

Examples

data(InputFile)
write.table(InputFile,"Input file.txt",sep="\t",na="",quote=FALSE,col.names=FALSE,row.names=FALSE)
read.frag.sizes("Input file.txt","25-2-2008","M1MpMetapop")

kkeenan02/MsatAllele documentation built on May 20, 2019, 10:42 a.m.