sommer (version 1.5)

atcg1234: Letter to number converter

Description

This function was designed to help users to transform their data in letter format to numeric format. Details in the format are not complex, just a dataframe with markers in columns and individuals in rows. Only markers, NO extra columns of plant names etc (names of plant can be stored as rownames).

Usage

atcg1234(data, ploidy=2, format="ATCG", maf=0, multi=TRUE)

Arguments

data

a dataframe with markers in columns and individuals in rows. Preferable the rownames are the ID of the plants so you don't lose track of what is what.

ploidy

a numeric value indicating the ploidy level of the specie. The default is 2 which means diploid.

format

one of the two possible values allowed by the program "ATCG", which means your calls are in base-pair-letter code, i.e. "AT" in a diploid call, "AATT" tetraploid etc (just example). Therefore possible codes can be "A", "T", "C", "G", "-" (deletion), "+" (

maf

minor allele frequency used to filter the SNP markers, the default is zero which means all markers are returned in numeric format.

multi

a TRUE/FALSE statement indicating if the function should get rid of the markers with more than 2 alleles. If FALSE, which indicates that if markers with multiple alleles are found, the alternate and reference alleles will be the first 2 alleles found. Thi

Value

• [object Object]

Examples

data(PolyData)
genotypes <- PolyData$PGeno
genotypes[1:5,1:5] # look the original format

####=================================================####
#### convert markers to numeric format polyploid potatoes
####=================================================####
#numo <- atcg1234(data=genotypes, ploidy=4)
#numo[1:5,1:5]; dim(numo)

####=================================================####
#### convert markers to numeric format diploid rice lines
####=================================================####
#data(RICE)
#X <- RICE$RiceGeno; X[1:5,1:5]; dim(X)
#numo2 <- atcg1234(data=X, ploidy=2)
#numo2[1:5,1:5]; dim(numo2)