2008-07-14

CFC program - Contribution, Inbreeding (F), Coancestry

It is quite some time since I downloaded the CFC program from here, see also here. However, I only tried to use it recently and found out that is quite handy. The program allows user to calculate:
  • inbreeding coefficients,
  • relationships (numerator or the "whole" relationship coefficient),
  • ancestral decomposition of inbreeding coefficients,
  • ancestral decomposition of the average coancestry,
  • optimization of matings to minimize the average inbreeding in the next generation,
  • probabilities of gene origin,
  • numerator relationship matrix, its decomposition and its inverse, and
  • recode the identifications from 1 to n (number of all individuals) in such a way that ancestors appear always before descendants.


A nice list of possible tasks for anyone working in genetics. It's GUI is very easy to use. It is a bit clumsy if you want to import the output to other program, say R. Therefore, I wrote two read.* functions that can import the output of numerator relationship matrix and its inverse into R.



read.CFCSparseA <- function(file, fileF=NULL, x, id, idI, out="dsCMatrix")
{
## ToDo: wrap into few lines - does it make any difference

## Read the numerator relationship matrix (A) from the CFC program
## - output in sparse format (triplets)
##
## file - character, name of the file with sparse matrix output from the CFC
## program (see bellow) non-inbred
## fileF - character, name of the file with inbreeding coefficients (see bellow)
## if NULL individuals are assumed
## x - data.frame, a pedigree with columns id (original identification) and
## idI (integer recoded identification)
## id - character, column name with original identification
## idI - character, column name with integer recoded identification
## out - character, "format" of the output: "triplet" (a data.frame) or
## "matrix" (a dsCMatrix)
##
## The file should contain only lines with the matrix elements i.e. without
## the header and footer lines. Edit the original output file to get file
## like this one (the first column is original subject identification, the
## second column is original subject identification, and the third column is
## non-zero matrix element):
##
## C A 0.5
## C B 0.5
## E A 0.25
## E B 0.25
## E D 0.5
## E C 0.5
##
## The fileF should have two columns: the first with original identification
## and the second with inbreeding coefficient of the individual:
##
## E 0.25
## F 0.05
##

require(Matrix)

## --- Check ---

## id and idI must be in the pedigree
tmp <- c(id, idI)
if(sum(tmp %in% names(x)) < 2) {
stop("wrong specification of id and/or idI column(s)")
}

## Output
tmp <- c("triplet", "dsCMatrix")
if(any(!(out %in% tmp))) {
stop(paste("out must be one of:", paste(tmp, collapse=", ")))
}

## Number of individuals
n <- as.integer(nrow(x))

## --- Import the datafile ---

tmp <- read.table(file=file)

## --- Match recoded identifications ---

tmp <- merge(tmp, x[, c(id, idI)], by.x="V1", by.y=id)
names(tmp)[names(tmp) %in% idI] <- "i"
tmp <- merge(tmp, x[, c(id, idI)], by.x="V2", by.y=id)
names(tmp)[names(tmp) %in% idI] <- "j"
names(tmp)[3] <- "x"
tmp[, 1] <- NULL
tmp[, 1] <- NULL

## --- Add diagonals = 1 + f ---

if(is.null(fileF)) { ## Assume that there is no inbreeding: diag(A) = 1
inbCoef <- x[, idI, drop=FALSE]
names(inbCoef) <- "i"
inbCoef$j <- inbCoef$i
inbCoef$x <- 1
tmp <- rbind(inbCoef[, c("x", "i", "j")], tmp)
} else { ## Get inbreeding coefficients: diag(A) = 1 + F
inbCoef <- read.table(file=fileF)[, 1:2]
names(inbCoef) <- c(id, "F")
inbCoef <- merge(inbCoef, x[, c(id, idI)], by.x=id, by.y=id, all.y=TRUE)
inbCoef[is.na(inbCoef[, "F"]), "F"] <- 0
inbCoef$j <- inbCoef[, idI]
inbCoef$F <- 1 + inbCoef[, "F"]
inbCoef[, 1] <- NULL
names(inbCoef) <- c("x", "i", "j")
tmp <- rbind(inbCoef, tmp)
}

## --- Return ---

if(out == "triplet") { ## Triplets: i, j, x
tmp[, c("i", "j", "x")]
} else { ## Symetric sparse matrix
as(new("dsTMatrix", Dim=c(n, n), uplo="L",
i=(tmp$i - 1L), j=(tmp$j - 1L), x=tmp$x), "dsCMatrix")
}
}



read.CFCSparseAInv <- function(file, out="dsCMatrix")
{
## ToDo: wrap into few lines - does it make any difference

## Read inverse of the numerator relationship matrix (A) from the CFC program
## - output in sparse format (triplets)
##
## file - character, name of the file with sparse matrix output from the CFC
## program
## out - character, "format" of the output: "triplet" (a data.frame) or
## "matrix" (a dsCMatrix)
##
## The file should contain only lines with the matrix elements i.e. without
## the header and footer lines. Edit the original output file to get file
## like this one (the first column is original subject identification, the
## second column is row index and the rest are column indexes, followed by a
## non-zero matrix element in the format columnIndex:non-zeroElement, ...):
##
## A, 1, 1:1.5,
## B, 2, 1:0.5, 2:1.5,
## D, 3, 3:1.5,
## F, 4, 4:1,
## C, 5, 1:-1, 2:-1, 3:0.5, 5:2.5,
## E, 6, 3:-1, 5:-1, 6:2,

require(Matrix)

## --- Check ---

tmp <- c("triplet", "dsCMatrix")
if(any(!(out %in% tmp))) {
stop(paste("out must be one of:", paste(tmp, collapse=", ")))
}

## --- Import and transformation ---

## A long "massage"
## 6. Split at each comma
tmp <- strsplit(split=",",
## 5. Remove the comma at the end
x=sub(pattern=",$", replacement="",
## 4. Change any colon to comma
x=gsub(pattern=":", replacement=",", fixed=TRUE,
## 3. Remove the first column (Individual ID) - ".," anything up to the first (since we use sub()) coma
x=sub(pattern=".,", replacement="",
## 2. Remove any spaces - " "
x=gsub(pattern=" ", replacement="", fixed=TRUE,
## 1. Read the file line by line
x=readLines(con=file))))))
## Number of rows = number of individuals
r <- as.integer(length(tmp))
## Length of each row
n <- sapply(tmp, length)
## Number of triplets by row - first element is a row index followed by a
## column index and a non-zero value
t <- (n - 1) %/% 2
## Number of all triplets; according to my tests, inverse of A has always at
## least one element per individual i.e. 1 for individuals without any relatives
N <- sum(t)
## Remove row index values
tmp <- lapply(tmp, function(z) z[-1])

## --- Build triplets ---

ret <- matrix(nrow=3, ncol=N)
## Row index
ret[1, ] <- rep(1:length(t), times=t)
## Column index and non-zero values
end <- cumsum(t)
start <- end - t + 1
i <- 1
while(i < (r + 1)) { ## Loop over all (r) individuals
ret[2:3, start[i]:end[i]] <- tmp[[i]]
i <- i + 1
}
## Modify for output
ret <- as.data.frame(t(matrix(as.numeric(ret), nrow=3, ncol=N, byrow=FALSE)))
names(ret) <- c("i", "j", "x")
ret[, 1:2] <- lapply(ret[, 1:2], as.integer)

## --- Return ---

if(out == "triplet") { ## Triplets: i, j, x
ret
} else { ## Symetric sparse matrix
as(new("dsTMatrix", Dim=c(r, r),
i=(ret$j - 1L), j=(ret$i - 1L), x=ret$x), "dsCMatrix")
}
}

2 comments:

laura said...

Dear Gregor, I need to use CFC but I can't find some help guide. For example, how is the imput file needed? I really apreciate your help! I´m a posgraduate student.

Gregor Gorjanc said...

There is a manual shipped with the program. Check the menus!