sidier (version 2.2)

HapPerPop: Returns the number of haplotypes per population.

Description

Given a two column matrix, this function returns the number of haplotypes per population. The input matrix must contain one row per individual. The first column must contain the population name, while the second must contain the name of the haplotype. The desired matrix can be obtained using "FindHaplo".

Usage

HapPerPop(inputFile = NA, sep = " ", header = F, input = NA,
NameIniPopulations = NA, NameEndPopulations = NA, saveFile = T,
Wname = NA, Iname = NA)

Arguments

inputFile

the name of the file containing the two columns input matrix.

sep

the character separating columns in the input matrix (space, by default).

header

a logical value indicating whether the input matrix contains the names of the variables as its first line. (Default=FALSE).

input

the two coumns input matrix stored in memory

NameIniPopulations

Position within the input matrix rownames of the initial character referring population origin.

NameEndPopulations

Position within the input matrix rownames of the last character referring population origin.

saveFile

a logical; if TRUE (default), the two ouput matrices computed are saved as two different text files.

Wname

the name given to the output weighted matrix file.

Iname

the name given to the output interaction matrix file

Value

• A list containing two matrices:
• Weighted
  The first matrix (named weighted matrix) contains the abundance of each haplotype per population, represented by the number of haplotypes (columns) found per population (rows).
• Interaction
  The second matrix (named interaction matrix) contains information about the presence or absence of each haplotype (columns) per population (rows) represented by 1 or 0, respectively.

Details

If both NameIniPopulations and NameEndPopulations are not defined, complete row names are used as population identifiers.

See Also

FindHaplo

Examples

cat("Sequence.Name Haplotype.Name",
"Population1 H1",
"Population1 H2",
"Population1 H3",
"Population1 H2",
"Population2 H4",
"Population2 H5",
"Population2 H6",
"Population2 H4",
"Population3 H7",
"Population3 H7",
"Population3 H7",
"Population3 H7",
     file = "3_FindHaplo_Example2_modified.txt", sep = "")

# Reading the alignment directly from file, displaying only the 
# weighted matrix:
	HapPerPop(inputFile="3_FindHaplo_Example2_modified.txt",header=TRUE,
saveFile=FALSE)[[1]]

# Reading the alignment from an object and saving the two computed
# distance matrices:
	FH<-read.table("3_FindHaplo_Example2_modified.txt",header=TRUE)
	HapPerPop(input=FH,header=TRUE,saveFile=FALSE)