initialise

.Rbuildignore

+^Readme\.Rmd$
+^\.travis\.yml$
+^_pkgdown\.yml$
+^docs$
+^cran-comments\.md$
+^appveyor\.yml$

.travis.yml

+# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
+
+language: R
+
+
+os:
+  - linux
+
+sudo: false	
+cache: packages
+use_bioc: true
+bioc_required: true
+
+r:
+  - devel
+
+r_packages:
+  - covr
+
+after_success:
+  - Rscript -e 'library(covr); codecov()'

DESCRIPTION

+Package: spliceQTL
+Version: 0.0.0
+Title: Alternative Splicing
+Description: Implements test for alternative splicing.
+Depends: R (>= 3.0.0)
+Imports: lme4, globaltest, edgeR, snpStats, refGenome, R.utils, methods
+Suggests: knitr, testthat
+Authors@R: c(person("Armin","Rauschenberger",email="a.rauschenberger@vumc.nl",role=c("aut","cre")),
+             person("Renee","Menezes",role=c("aut")))
+VignetteBuilder: knitr
+License: GPL-3
+LazyData: true
+RoxygenNote: 6.0.1
+URL: https://github.com/rauschenberger/spliceQTL
+BugReports: https://github.com/rauschenberger/spliceQTL/issues

NAMESPACE

+# Generated by roxygen2: do not edit by hand
+
+export(adjust.exon.length)
+export(adjust.library.sizes)
+export(drop.trivial.genes)
+export(map.exons)
+export(map.genes)
+export(map.snps)
+export(prepare.data.matrices)
+export(spliceQTL)

NEWS.md

+## spliceQTL 0.0.0 (2018-06-12)
+
+* Added functions
\ No newline at end of file

R/function.R

+
+#' @export
+#' @title
+#' Prepare data matrices
+#' 
+#' @description
+#' This function removes duplicate samples, retains overlapping samples, and
+#' orders samples.
+#' 
+#' @param Y
+#' matrix with \eqn{n_y} rows (samples) and \eqn{p_y} columns (exons)
+#' 
+#' @param X
+#' matrix with \eqn{n_x} rows (samples) and \eqn{p_x} columns (SNPs)
+#' 
+#' @examples
+#' NA
+#' 
+prepare.data.matrices <- function(Y,X){
+    
+    # check input
+    if(!is.matrix(Y)|!is.matrix(X)){
+        stop("Provide X and Y as matrices!",call.=FALSE)
+    }
+    if(is.null(rownames(Y))|is.null(rownames(X))){
+        stop("Missing sample names!",call.=FALSE)
+    }
+    
+    # remove duplicate samples
+    dup_y <- duplicated(rownames(Y))
+    dup_x <- duplicated(rownames(X))
+    message("Duplicates: removing ",round(mean(dup_y),2),"% of Y.")
+    message("Duplicates: removing ",round(mean(dup_x),2),"% of X.")
+    Y <- Y[!dup_y,]
+    X <- X[!dup_x,]
+    
+    # retain overlapping samples
+    both <- intersect(x=rownames(Y),y=rownames(X))
+    message("Overlap: retaining ",round(mean(rownames(Y) %in% both),2),"% of Y.")
+    message("Overlap: retaining ",round(mean(rownames(X) %in% both),2),"% of X.")
+    Y <- Y[both,]
+    X <- X[both,]
+    
+    # check output
+    if(any(duplicated(rownames(Y))) | any(duplicated(rownames(X)))){
+        stop("Duplicate samples!",call.=FALSE)
+    }
+    if(nrow(Y)!=nrow(X)){
+        stop("Different sample sizes!",call.=FALSE)
+    }
+    if(any(rownames(Y)!=rownames(X))){
+        stop("Different sample names!",call.=FALSE)
+    }
+    
+    return(list(Y=Y,X=X))
+}
+
+
+#' @export
+#' @title
+#' Adjust library sizes
+#' 
+#' @description
+#' This function adjusts exon expression data for different library sizes.
+#' 
+#' @param y
+#' matrix with \eqn{n} rows (samples) and \eqn{p} columns (exons)
+#' 
+#' @examples
+#' NA
+#' 
+adjust.library.sizes <- function(y){
+    n <- nrow(y); p <- ncol(y)
+    lib.size <- colSums(y)
+    norm.factors <- edgeR::calcNormFactors(object=y,lib.size=lib.size)
+    gamma <- norm.factors*lib.size/mean(lib.size)
+    gamma <- matrix(gamma,nrow=p,ncol=n,byrow=TRUE)
+    return(y/gamma)
+}
+
+#' @export
+#' @title
+#' Adjust exon length
+#' 
+#' @description
+#' This function adjusts exon expression data for different exon lengths.
+#' 
+#' @param y
+#' matrix with \eqn{n} rows (samples) and \eqn{p} columns (exons)
+#' 
+#' @param gene
+#' gene (not exon) names\strong{:} vector of length \eqn{p}
+#' 
+#' @param start
+#' exon start positions\strong{:} vector of length \eqn{p}
+#' 
+#' @param end
+#' exon end positions\strong{:} vector of length \eqn{p}
+#' 
+#' @details
+#' No information on chromosomes required.
+#' 
+#' @examples
+#' NA
+#' 
+adjust.exon.length <- function(y,gene,start,end){
+    n <- nrow(y); p <- ncol(y); names <- dimnames(y)
+    y <- as.numeric(y)
+    x <- rep(end-start,times=n)
+    gene <- rep(gene,times=n)
+    lmer <- lme4::lmer(y ~ x + (1|gene))
+    y <- matrix(stats::residuals(lmer),nrow=p,ncol=n,dimnames=names)
+    return(y - min(y))
+}
+
+#' @export
+#' @title
+#' Search for genes
+#' 
+#' @description
+#' This function retrieves all genes on a chromosome.
+#' 
+#' @param chr
+#' chromosome\strong{:} integer 1-22
+#' 
+#' @param path
+#' path to gene transfer format files (.gtf)
+#' 
+#' @param release
+#' character "NCBI36", "GRCh37", or "GRCh38"
+#' 
+#' @param build
+#' integer 49-91
+#' 
+#' @details
+#' This functions ...
+#' 
+#' @examples
+#' NA
+#' 
+map.genes <- function(chr,path=getwd(),release="GRCh37",build="71"){
+    file <- paste0("Homo_sampiens.",release,".",build,".gtf")
+    if(!file.exists(file)){
+        url <- paste0("ftp://ftp.ensembl.org/pub/release-",build,
+                      "/gtf/homo_sapiens/",file,".gz")
+        destfile <- file.path(path,paste0(file,".gz"))
+        utils::download.file(url=url,destfile=destfile,method="auto")
+        R.utils::gunzip(filename=destfile,remove=FALSE,overwrite=TRUE)
+    }
+    object <- refGenome::ensemblGenome()
+    refGenome::basedir(object) <- path
+    refGenome::read.gtf(object,filename=file)
+    genes <- refGenome::getGenePositions(object=object,by="gene_id")
+    genes <- genes[genes$seqid==chr & genes$gene_biotype=="protein_coding",]
+    genes <- genes[,c("gene_id","seqid","start","end")]
+    colnames(genes)[colnames(genes)=="seqid"] <- "chr"
+    return(genes)
+}
+
+#' @export
+#' @title
+#' Search for exons
+#' 
+#' @description
+#' This function
+#' 
+#' @param gene_id
+#' gene names\strong{:} vector with one entry per gene
+#' 
+#' @param exon_id
+#' exon names\strong{:} vector with one entry per exon
+#' 
+#' @details
+#' The exon names should contain the gene names. For each gene, this function
+#' returns the indices of the exons.
+#' 
+#' @examples
+#' NA
+#'
+map.exons <- function(gene_id,exon_id){
+    if(length(gene_id)!=length(exon_id)){stop("Invalid.",call.=FALSE)}
+    p <- length(gene_id)
+    exons <- list()
+    pb <- utils::txtProgressBar(min=0,max=p,style=3)
+    for(i in seq_len(p)){
+        utils::setTxtProgressBar(pb=pb,value=i)
+        which <- as.integer(grep(pattern=gene_id[i],x=exon_id)) # Why not "=="?
+        exons[[i]] <- which
+    }
+    return(exons)
+}
+
+#' @export
+#' @title
+#' Search for SNPs
+#' 
+#' @description
+#' This function
+#' 
+#' @param gene.chr
+#' chromosome\strong{:}
+#' numeric vector with one entry per gene
+#' 
+#' @param gene.start
+#' start position\strong{:}
+#' numeric vector with one entry per gene
+#' 
+#' @param gene.end
+#' end position\strong{:}
+#' numeric vector with one entry per gene
+#' 
+#' @param snp.chr
+#' integer 1-22
+#' 
+#' @param snp.pos
+#' chromosomal position of SNPs\strong{:}
+#' numeric vector with one entry per SNP
+#' 
+#' @details
+#' This functions ...
+#' 
+#' @examples
+#' NA
+#' 
+map.snps <- function(gene.chr,gene.start,gene.end,snp.chr,snp.pos){
+    if(length(gene.chr)!=length(gene.start)|length(gene.chr)!=length(gene.end)){
+        stop("Invalid.",call.=FALSE)
+    }
+    p <- length(gene.start)
+    snps <- data.frame(from=integer(length=p),to=integer(length=p))
+    pb <- utils::txtProgressBar(min=0,max=p,style=3)
+    for(i in seq_len(p)){ # 
+        utils::setTxtProgressBar(pb=pb,value=i)
+        chr <- snp.chr == gene.chr[i]
+        if(!any(chr)){next}
+        start <- snp.pos >= gene.start[i] - 1*10^3
+        end <- snp.pos <= gene.end[i] + 0
+        which <- as.integer(which(chr & start & end))
+        if(length(which)==0){next}
+        snps$from[i] <- min(which)
+        snps$to[i] <- max(which)
+        if(length(which)==1){next}
+        if(!all(diff(which)==1)){stop("SNPs are in wrong order!")}
+    }
+    return(snps)
+}
+
+#' @export
+#' @title
+#' Drop "trivial" genes
+#' 
+#' @description
+#' This function
+#' 
+#' @param map
+#' list with names "genes", "exons", and "snps"
+#' (output from \code{map.genes}, \code{map.exons}, and \code{map.snps})
+#' 
+#' @details
+#' This functions drops genes without SNPs or with a single exon.
+#' 
+#' @examples
+#' NA
+#' 
+drop.trivial.genes <- function(map){
+    p <- length(map$genes)
+    pass <- rep(NA,times=p)
+    pb <- utils::txtProgressBar(min=0,max=p,style=3)
+    for(i in seq_len(p)){ # seq_len(p)
+        utils::setTxtProgressBar(pb=pb,value=i)
+        ys <- map$exons[[i]]
+        check <- logical()
+        # Exclude genes without SNPs:
+        check[1] <- map$snps$from[i] > 0
+        check[2] <- map$snps$to[i] > 0
+        # Exclude genes with single exon:
+        check[3] <- length(ys) > 1
+        pass[i] <- all(check)
+    }
+    map$genes <- map$genes[pass,]
+    map$exons <- map$exons[pass]
+    map$snps <- map$snps[pass,]
+    return(map)
+}
+
+
+#' @export
+#' @title
+#' Conduct tests
+#' 
+#' @description
+#' This function
+#' 
+#' @param Y
+#' exon expression\strong{:}
+#' matrix with \eqn{n} rows (samples) and \eqn{p} columns (exons)
+#' 
+#' @param X
+#' SNP genotype\strong{:}
+#' matrix with \eqn{n} rows (samples) and \eqn{q} columns (SNPs)
+#' 
+#' @param map
+#' list with names "genes", "exons", and "snps"
+#' (output from \code{map.genes}, \code{map.exons}, and \code{map.snps})
+#' 
+#' @param i
+#' gene index\strong{:}
+#' integer between \eqn{1} and \code{nrow(map$genes)}
+#' 
+#' @param limit
+#' cutoff for rounding \code{p}-values
+#' 
+#' @param steps
+#' size of permutation chunks\strong{:}
+#' integer vector
+#' 
+#' @details
+#' The maximum number of permutations equals \code{sum(steps)}. Permutations is
+#' interrupted if at least \code{limit} test statistics for the permuted data
+#' are larger than the test statistic for the observed data.
+#' 
+#' @examples
+#' NA
+#' 
+spliceQTL <- function(Y,X,map,i,limit,steps){
+    
+    ### extraction ###
+    ys <- map$exons[[i]]
+    y <- list()
+    y$norm <- t(as.matrix(Y$norm[ys,,drop=FALSE]))
+    y$counts <- t(Y$counts[ys,,drop=FALSE])
+    xs <- seq(from=map$snps$from[i],to=map$snps$to[i],by=1)
+    x <- methods::as(X$genotypes[,xs],"numeric")
+    pvalue <- list()
+    
+    ### level 1: spliceQTL test ###
+    for(type in c("norm","counts")){
+        for(rho in c(0,0.2,0.5,1)){
+            tstat <- G2.multin(dep.data=y[[type]],indep.data=x,
+                               nperm=steps[1]-1,rho=rho)$Sg
+            for(nperm in steps[-1]){
+                tstat <- c(tstat,G2.multin(dep.data=y[[type]],indep.data=x,
+                                           nperm=nperm,rho=rho)$Sg[-1])
+                if(sum(tstat >= tstat[1]) >= limit){break}
+            }
+            pvalue[[paste(type,rho,sep="")]] <- 
+                mean(tstat >= tstat[1],na.rm=TRUE)
+        }
+    }
+    
+    #### level 2: global test ###
+    pvalue$global <- rep(NA,times=length(ys))
+    for(j in seq_along(ys)){
+        gt <- globaltest::gt(response=y$norm[,j],alternative=x)
+        pvalue$global[j] <- globaltest::p.value(gt)
+    }
+    
+    ### level 3: pairwise test ###
+    pvalue$pair <- matrix(NA,nrow=length(ys),ncol=length(xs))
+    for(j in seq_along(ys)){
+        for(k in seq_along(xs)){
+            lm <- stats::lm(y$norm[,j] ~ x[,k])
+            pvalue$pair[j,k] <- summary(lm)$coef["x[, k]","Pr(>|t|)"]
+        }
+    }
+    
+    return(pvalue)
+}
+
+
+
+#--- spliceQTL test functions --------------------------------------------------
+
+# Function: G2.multin
+# This is to compute the G2 test statistic under the assumption that the response follows a multinomial distribution
+### Input 
+### dep data and indep data with samples on the rows and genes on the columns
+### grouping: Either a logical value = F or a matrix with a single column and same number of rows as samples. 
+###         Column name should be defined.
+###         Contains clinical information of the samples. 
+###         Should have two groups only. 
+### nperm : number of permutations 
+### rho: the null correlation between SNPs
+### mu: the null correlation between observations corresponding to different exons and different individuals
+
+### Output
+### A list containing G2 p.values and G2 test statistics
+
+### Example : G2T = G2(dep.data = cgh, indep.data = expr, grouping=F, stand=TRUE, nperm=1000)
+### G2 p.values : G2T$G2p
+### G2 TS : G2T$$Sg
+
+G2.multin <- function(dep.data,indep.data,stand = TRUE, nperm=100,grouping=F,rho=0,mu=0){
+    
+    nperm = nperm
+    ## check for the number of samples in dep and indep data
+    
+    
+    if (nrow(dep.data)!=nrow(indep.data)){
+        cat("number of samples not same in dep and indep data","\n")
+    }
+    
+    if(any(abs(rho)>1)){
+        cat("correlations rho larger than abs(1) are not allowed")
+    }
+    
+    nresponses <- ncol(dep.data)
+    ncovariates <- ncol(indep.data)
+    ### centering and standardizing the data are not done in this case
+    
+    #  dep.data = scale(dep.data,center=T,scale=stand)
+    #  indep.data = scale(indep.data,center=T,scale=stand)
+    
+    #### No  grouping of the samples.
+    
+    ## Calculate U=(I-H)Y and UU', where Y has observations on rows; also tau.mat=X*W.rho*X', 
+    ##   where X has observations on rows and variables on columns
+    ##  and W.rho = I + rho*(J-I), a square matrix with as many rows as columns in X
+    ## NOTE: this formulation uses X with n obs on the rows and m covariates no the columns, so it is the transpose of the first calculations
+    nsamples <- nrow(dep.data)
+    n.persample <- rowSums(dep.data)
+    n.all <- sum(dep.data)
+    H <- (1/n.all)*matrix( rep(n.persample,each=nsamples),nrow=nsamples,byrow=T)
+    U <- (diag(rep(1,nsamples)) - H) %*% dep.data
+    ## Now we may have a vector of values for rho - so we define tau.mat as an array, with the 3rd index corresponding to the value of rho
+    tau.mat <- array(0,dim=c(nsamples,nsamples,length(rho)))
+    for(xk in 1:length(rho))  
+    {  
+        if (rho[xk]==0) { tau.mat[,,xk] <- tcrossprod(indep.data) } 
+        else { w.rho <- diag(rep(1,ncovariates)) + rho[xk]*(tcrossprod(rep(1,ncovariates)) -diag(rep(1,ncovariates))  )
+        tau.mat[,,xk] <- indep.data %*% w.rho %*% t(indep.data)}
+        
+    }
+    ######################################
+    ### NOTES ARMIN START ################
+    # all(X %*% t(X) == tau.mat[,,1]) # rho = 0 -> TRUE
+    # all(X %*% (t(X) %*% X) %*% t(X) == tau.mat[,,1]) # rho = 1
+    # plot(as.numeric(X %*% (t(X) %*% X) %*% t(X)),as.numeric(tau.mat[,,1]))
+    ### NOTES ARMIN END ##################
+    ######################################
+    samp_names = 1:nsamples ## this was rownames(indep.data), but I now do this so that rownames do not have to be added to the array tau.mat
+    Sg = get.g2stat.multin(U,mu=mu,rho=rho,tau.mat)
+    ### now we will have a vector as result, with one value per combination of values of rho and mu
+    #
+    ### G2 
+    ### Permutations
+    # When using permutations: only the rows of tau.mat are permuted
+    # To check how the permutations can be efficiently applied, see tests_permutation_g2_multin.R
+    
+    
+    perm_samp = matrix(0, nrow=nrow(indep.data), ncol=nperm)   ## generate the permutation matrix
+    for(i in 1:ncol(perm_samp)){
+        perm_samp[,i] = samp_names[sample(1:length(samp_names),length(samp_names))]
+    }
+    
+    ## permutation starts - recompute tau.mat  (or recompute U each time)
+    for (perm in 1:nperm){
+        tau.mat.perm = tau.mat[perm_samp[,perm],,,drop=FALSE]          # permute rows
+        tau.mat.perm = tau.mat.perm[,perm_samp[,perm],,drop=FALSE]     # permute columns
+        
+        Sg = c(Sg, get.g2stat.multin(U, mu=mu,rho=rho,tau.mat.perm) )
+    }
+    
+    
+    ########################################################################
+    
+    #### G2 test statistic
+    # *** recompute for a vector of values for each case - just reformat the result with as many rows as permutations + 1,
+    # and as many columns as combinations of values of rho and mu
+    Sg = matrix(Sg,nrow=nperm+1,ncol=length(mu)*length(rho))
+    colnames(Sg) <- paste(rep("rho",ncol(Sg)),rep(1:length(rho),each=length(mu)),rep("mu",ncol(Sg)),rep(1:length(mu),length(rho)) )
+    
+    ### Calculte G2 pval
+    G2p =  apply(Sg,2,get.pval.percol) 
+    
+    return (list(perm = perm_samp,G2p = G2p,Sg = Sg))
+}
+
+# Function: get.g2stat.multin
+# Computes the G2 test statistic given two data matrices, under a multinomial distribution
+# This is used internally by the G2 function
+# Inputs: 
+#  U = (I-H)Y, a n*K matrix where n=number obs and K=number multinomial responses possible
+#  tau.mat = X' W.rho X, a n*n matrix : both square, symmetric matrices with an equal number of rows
+# Output: test statistic (single value)
+# 
+get.g2stat.multin <- function(U, mu, rho, tau.mat)
+{
+    g2tstat <- NULL
+    for(xk in 1:length(rho))
+    {
+        for(xj in 1:length(mu))
+        {
+            if(mu[xj]==0) { g2tstat <- c(g2tstat, sum( diag( tcrossprod(U) %*% tau.mat[,,xk] ) ) )
+            } else {
+                g2tstat <- c(g2tstat, (1-mu[xj])*sum(diag( tcrossprod(U) %*% tau.mat[,,xk] ) ) + mu[xj]*sum( t(U) %*% tau.mat[,,xk] %*% U )  )
+            }
+            
+        }
+    }
+    g2tstat
+}
+
+# Function: get.pval.percol
+# This function takes a vector containing the observed test stat as the first entry, followed by values generated by permutation,
+# and computed the estimated p-value
+# Input
+# x: a vector with length nperm+1
+# Output
+# the pvalue computed
+get.pval.percol <- function(x){
+    pval = mean(x[1]<= c(Inf , x[2:length(x)]))
+    pval
+}
+

README.Rmd

+
+---
+output: github_document
+---
+
+<!-- Modify xxx.Rmd, not xxx.md! -->
+
+```{r, echo = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "README-"
+)
+```
+
+## Scope
+
+spliceQTL
+
+## Installation
+
+```{r,eval=FALSE}
+#install.packages("devtools")
+devtools::install_github("rauschenberger/spliceQTL")
+```
+
+## Reference
+
+

README.md

+
+<!-- Modify xxx.Rmd, not xxx.md! -->
+
+## Scope
+