transcript_GC: Transcript GenClone files

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

View source: R/RClone.R

Description

transcript_GC allows conversion from GenClone files to RClone files.

Usage

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transcript_GC(obj, ele, num1, num2, num3)

Arguments

obj

a .csv file from GenClone (.txt saved as .csv).

ele

option, separator element for import.

num1

numeric, the number of loci.

num2

numeric, the ploidy level. 2 for diploids and 1 for haploids.

num3

numeric, the length of each allele.

Details

GenClone files are generally .txt files named infile.txt. You must save it as .csv file with ";" as separators and, if necessary, change "," by ".".

Value

transcript_GC returns a list of:

data_genet

a table of genotypes, one allele per column and one unit per row,

data_coord

a table of x/y coordinates,

names_loci

a vector of names of the loci,

names_units

a vector of names of the units.

Note

transcript_GC works only with infile files full of informations (loci names, ploidy names, etc.).

Author(s)

Creator/Author: Diane Bailleul <[email protected]>
Author: Sophie Arnaud-Haond <[email protected]>
Contributor: Solenn Stoeckel

The R implementation of RClone was written by Diane Bailleul.

The design was inspired by GenClone program described in Arnaud-Haond & Belkhir (2007).

References

Arnaud-Haond et al., 2007, Standardizing methods to address clonality in population studies.

See Also

sort_all for sorting users tables with one allele per column.

Examples

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data(infile)
#This is nearly a GenClone file, type:
#write.table(infile, "infile.csv", col.names = FALSE, row.names = FALSE, sep = ";")
#Now you have a formatted GenClone file:
#res <- transcript_GC("infile.csv", ";", 2, 7, 3)
#data1 <- res$data_genet
#coord <- res$data_coord

dbailleul/RClone documentation built on May 12, 2017, 8:56 p.m.