R/gwas.cross.R

In lmem.gwaser: Linear Mixed Effects Models for Genome-Wide Association Studies

#########################################
#' Read genomic data to perform GWAS analyses.
#'
#' This function reads genomic data and is similar to the read.cross
#' function from r/qtl package (Broman and Sen, 2009) but allows
#' importing data from a flapjack format (Milne et al., 2010).
#' Additionally, it loads diverse populations for GWAS analysis
#' into r/qtl format. The files required include a file containing phenotypic
#' information (P.data), a file containing genotypic information (G.data),
#' and a file containing map information (map.data) for all markers.
#'
#' @param P.data Name of the file containing phenotypic information.
#'Each row represents the individuals while each column represents
#'the phenotypic traits. The first column should be labeled as 'genotype'
#'and should contain identification name for each individual.
#'The name of each trait should also be included.
#'
#' @param G.data Name of the file containing genotypic (marker scores)
#'information. Each row represents the individuals
#'while each column represents the markers. Headers for markers should be
#'included, but not for genotypes.
#'The first column contains the names of the genotypes.
#'The first row contains the names of the markers.
#'The marker genotypes are coded by two characters corresponding
#'to the alleles using a separator between alleles (by default a slash /).
#'If a single character is given, the genotype is assumed to be homozygous.
#'Missing values are indicated by default with '-'.
#'In the example below, the two alleles have been called 1 and 2 because it
#'is useful to link alleles to their origin, i.e. parent 1 or parent 2.
#'Therefore, 1 corresponds to homozygous for allele 1 (synonymous to 1/1),
#'1/2 corresponds to heterozygous, and 2 corresponds to homozygous
#'for allele 2 (synonymous to 2/2).
#'In the case of partially informative markers (e.g. dominant markers)
#'genotypes are coded as 1/- or 2/-, depending on whether the dominant
#'allele originated from parent 1 or parent 2.
#'
#' @param  map.data Name of the file containing marker map information (
#' i.e. linkage group and position within linkage group).
#' The file is a text tab delimited file. Each row represents markers.
#' The file consists of three columns.
#' Column 1 gives the marker names,
#' column 2 the chromosome on which the marker has been mapped,
#' and column 3 indicates the position of the marker within the chromosome.
#'
#' @param cross The type of population studied. gwas is set as default
#' Diverse population panel for GWAS.
#'
#' @param heterozygotes It indicates whether there are heterozygotes or
#' not in the association mapping population. TRUE is set as default.
#'
#'
#' @param sep To define the espace between the data.
#'
#' @return Creates an object of class cross to be used in GWAS analysis. The component
#' are  the same as r/qtl (Broman and Sen, 2009): geno
#'
#' @references Broman KW, Sen S (2009) A Guide to QTL Mapping with R/qtl.
#'             Springer, NewYork
#'             Comadran J, Thomas W, van Eeuwijk F, Ceccarelli S, Grando S, Stanca A,
#'             Pecchioni N, Akar T, Al-Yassin A, Benbelkacem A, Ouabbou H, Bort J,
#'             Romagosa I, Hackett C, Russell J (2009) Patterns of genetic diversity
#'             and linkage disequilibrium in a highly structured Hordeum vulgare
#'             association-mapping population for the Mediterranean basin.
#'             Theor Appl Genet 119:175-187
#'             Milne et al., (2010) Flapjack - graphical genotype visualization.
#'             Bioinformatics 26(24), 3133-3134.
#'
#' @author Lucia Gutierrez, Gaston Quero.
#'
#' @details The function creates an intermediate file called 'temp.csv' and
#' then uses the read.cross from r/qtl to read it.
#' The output object is an object of class=cross, the same as the
#' one produced by the function read.cross in r/qtl (Broman and Sen, 2009)
#'
#' @note All functions in this package uses cross data style.
#'
#' @seealso gwas.analysis
#' @import qtl
#' @import grDevices
#' @import graphics
#' @import stats
#' @import utils
#'
#' @export
#'
#' @examples
#' data (QA_geno)
#' data (QA_map)
#' data (QA_pheno)
#'
#' P.data <- QA_pheno
#' G.data <- QA_geno
#' map.data <- QA_map
#'
#' cross.data <- gwas.cross (P.data, G.data, map.data,
#' cross='gwas', heterozygotes=FALSE)
#'
#' summary (cross.data)
#'
gwas.cross <- function(P.data = NULL, G.data, map.data, cross = "gwas",
                        heterozygotes = TRUE, sep = "\t") {
    cross.data <- NULL

    G.data <- as.matrix(G.data)
    G.data[G.data == " 0"] <- "0"
    G.data[G.data == " 1"] <- "1"

    G.data <- G.data[which(G.data[, 1] %in% as.character(P.data$genotype)), ]
    P.data <- P.data[which(as.character(P.data$genotype) %in% G.data[, 1]), ]
    rownames(G.data) <- G.data[, 1]
    G.data <- G.data[, 2:ncol(G.data)]

    G.data <- G.data[, which(colnames(G.data) %in% map.data[, 1])]
    map.data <- map.data[which(map.data[, 1] %in% colnames(G.data)), ]
    G.data <- G.data[, match(map.data[, 1], colnames(G.data))]

    P.data <- P.data[match(rownames(G.data), as.character(P.data$genotype)), ]

    a <- matrix(rep("", (ncol(P.data) * 2)), 2, ncol(P.data))

    colnames(a) <- colnames(P.data)

    names(a) <- names(P.data)

    b <- data.frame(t(map.data[, 2:3]))

    names(b) <- as.character(map.data[, 1])

    c <- data.frame(a, b, check.names = FALSE, stringsAsFactors = FALSE)

    rownames(c) <- c(rownames(a), rownames(b))

    # extract id information for geno and pheno
    G.id <- row.names(G.data)
    P.id <- as.character(P.data$genotype)

    if (sum(G.id != P.id) > 0) {
        simpleError("IDs don't match")
    }

    geno.data <- G.data

    gens <- c(unlist(geno.data))
    gens <- sort(unique(gens[gens != "-"]))

    als <- unique(c(unlist(strsplit(gens, "/"))))

    Het <- gens[which(gens == paste(als[1], als[2], sep = "/") | gens == paste(als[2], als[1],
        sep = "/"))]
    if (length(Het) > 0) {
        hetpos <- grep(Het, geno.data)
        Apos <- setdiff(grep(als[1], geno.data), hetpos)
        Bpos <- setdiff(grep(als[2], geno.data), hetpos)
        geno.data[hetpos] <- "1/2"
    }
    if (length(Het) == 0) {
        Apos <- grep(als[1], geno.data)
        Bpos <- grep(als[2], geno.data)
    }
    geno.data[Apos] <- "1/1"
    geno.data[Bpos] <- "2/2"
    geno.data[geno.data == "1/1"] <- "AA"
    geno.data[geno.data == "2/2"] <- "BB"
    geno.data[geno.data == "1/2"] <- "AB"
    geno.data[geno.data == "1/-"] <- "C"
    geno.data[geno.data == "2/-"] <- "D"
    geno.data[geno.data == "-"] <- NA

    e <- cbind(P.data, geno.data)

    f <- rbind(c, e)

    names(f)[1] <- "id"

    zz <- file("cross.data.file.csv", "w")

    write.csv(f, zz, quote = FALSE, row.names = FALSE)

    close(zz)

    if (cross == "gwas") {
        gwas <- "gwas"
    }

    if (cross == "gwas" & heterozygotes == "FALSE") {
        cross <- "dh"
    }

    if (cross == "gwas" & heterozygotes == "TRUE") {
        cross <- "f2"
    }

    # this is to import the cross

    if (cross == "dh")
        {
            cross.data <- read.cross("csv", file = "cross.data.file.csv", genotypes = c("AA",
                "BB"))
        }  #check if more

    if (cross == "f2") {
        cross.data <- read.cross("csv", file = "cross.data.file.csv", genotypes = c("AA", "AB",
            "BB", "C", "D"))
    }

    class(cross.data)[1] <- paste(cross)

    if (gwas == "gwas") {
        cross.data$gwas <- "gwas"
    }

    cross.data

}